Why the input needs different format of sam and bam?

[DadongZ]

According to the manual of JUM 2.0.2: Under your working folder (/user/home/AS_analysis), you should have the following input files ready for JUM analysis ("" indicates ctrl1, ctrl2, ctrl3, treat1, treat2 and treat3): Aligned.out.sam files SJ.out.tab files Aligned.out_sorted.bam files

Why does it require different format: sam for Aligned.out.sam and bam for Aligned.out_sorted.bam? All of my STAR output were in bam format and the program turned out unable to find the .Aligned.out.sam. I am wondering whether I should convert them to sam format.

[qqwang-berkeley]

Hi,

There are two separate step in JUM_A.sh, one extracting information directly from Aligned.out.sam file and the other transforming Aligned.out_sorted.bam. In the next update I will combine the two steps so that users only need to have the bam files for the downstream process. But for now you do need to have both...

Thank you for the feedback. Let me know if you have any questions.

Qingqing

On Tue, Apr 23, 2019 at 8:26 AM DadongZhang notifications@github.com wrote:

According to the manual of JUM 2.0.2: Under your working folder (/user/home/AS_analysis), you should have the following input files ready for JUM analysis ("" indicates ctrl1, ctrl2, ctrl3, treat1, treat2 and treat3): Aligned.out.sam files SJ.out.tab files Aligned.out_sorted.bam files

Why does it require different format: sam for *Aligned.out.sam and bam for Aligned.out_sorted.bam?

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[DadongZ]

Thanks for your reply. I got the follow issue regarding space limit. I thought it might be related to java or perl and trying to locate the script line to make some changes. Do you have some suggestions:

Sample names are:
4654-S113_S17_L001
4654-S114_S18_L001
4654-S115_S19_L001
4654-S116_S20_L001
4654-S117_S21_L001
4654-S118_S22_L001
4654-S119_S23_L001
4654-S120_S24_L001
4654-S129_S33_L001
4654-S130_S34_L001
4654-S131_S35_L001
4654-S132_S36_L001
4654-S133_S37_L001
4654-S134_S38_L001
4654-S135_S39_L001
4654-S136_S40_L001
8 input samples to consider under the current condition
8 input samples to consider under the current condition
Preparing for intron retention AS events analyses...
Processing junction overhangs for Sample 4654-S131_S35_L001... Success.
Processing junction overhangs for Sample 4654-S135_S39_L001... Success.
Processing junction overhangs for Sample 4654-S129_S33_L001... Success.
Processing junction overhangs for Sample 4654-S133_S37_L001... Success.
Processing junction overhangs for Sample 4654-S132_S36_L001... Success.
Processing junction overhangs for Sample 4654-S130_S34_L001... Success.
Processing junction overhangs for Sample 4654-S119_S23_L001... Success.
Processing junction overhangs for Sample 4654-S117_S21_L001... Success.
Processing junction overhangs for Sample 4654-S113_S17_L001... Success.
Processing junction overhangs for Sample 4654-S116_S20_L001... Success.
Processing junction overhangs for Sample 4654-S136_S40_L001... Success.
Processing junction overhangs for Sample 4654-S114_S18_L001... Success.
Processing junction overhangs for Sample 4654-S134_S38_L001... Success.
Processing junction overhangs for Sample 4654-S115_S19_L001... Success.
Processing junction overhangs for Sample 4654-S120_S24_L001... Success.
Processing junction overhangs for Sample 4654-S118_S22_L001... Success.
sort: write failed: /tmp/sortyDi2zy: No space left on device
sort: write failed: /tmp/sortW6Z6Pdsort: write failed: /tmp/sort4J3w93: No space left on device
: No space left on device
4654-S113_S17_L001
4654-S114_S18_L001
4654-S115_S19_L001
cp: cannot stat '4654-S116_S20_L001_junction_counts_combined_intron_retention_event_list.txt': No such file or directory

I was running it on server and the program may be looking for my home directory's tmp and that usually have limited space. It would be helpful to point me how to set it to other directory (with large space).

[qqwang-berkeley]

Yes I have seen this kind of problems reported by users before and it can be settled quickly,

This is caused by the Linux command "sort", which usually has a default "temporary" folder that it uses to write temporary files. The default temporary folder is usually set right under the home directory, which in your case is the main drive and quickly ran out of space when you are dealing with huge files.

What you can do, is to direct the default temporary folder of "sort" into a different directory, which has more space. Use the following command:

export TMPDIR=/home/temporary

(I made up the directory /home/temporary, you need to change it into the actual path of your local drive).

The TMPDIR environment variable is what "sort" responds to and it will reset its temporary writing folder to the temporary directory.

Also, note that once set, the change will carry on for the current log in session. If you log out of linux terminal and come back again, you need to type it again for the change to work.

A quick way to see if the change works or not is to type:

echo TMPDIR

Then linux will tell you what the current setting for the "sort" temporary writing folder is.

Let me know how it works and if this solves the problem.

On Tue, Apr 30, 2019 at 6:29 AM DadongZhang notifications@github.com wrote:

Thanks for your reply. I got the follow issue regarding space limit. I thought it might be related to java or perl and trying to locate the script line to make some changes. Do you have some suggestions:

Sample names are: 4654-S113_S17_L001 4654-S114_S18_L001 4654-S115_S19_L001 4654-S116_S20_L001 4654-S117_S21_L001 4654-S118_S22_L001 4654-S119_S23_L001 4654-S120_S24_L001 4654-S129_S33_L001 4654-S130_S34_L001 4654-S131_S35_L001 4654-S132_S36_L001 4654-S133_S37_L001 4654-S134_S38_L001 4654-S135_S39_L001 4654-S136_S40_L001 8 input samples to consider under the current condition 8 input samples to consider under the current condition Preparing for intron retention AS events analyses... Processing junction overhangs for Sample 4654-S131_S35_L001... Success. Processing junction overhangs for Sample 4654-S135_S39_L001... Success. Processing junction overhangs for Sample 4654-S129_S33_L001... Success. Processing junction overhangs for Sample 4654-S133_S37_L001... Success. Processing junction overhangs for Sample 4654-S132_S36_L001... Success. Processing junction overhangs for Sample 4654-S130_S34_L001... Success. Processing junction overhangs for Sample 4654-S119_S23_L001... Success. Processing junction overhangs for Sample 4654-S117_S21_L001... Success. Processing junction overhangs for Sample 4654-S113_S17_L001... Success. Processing junction overhangs for Sample 4654-S116_S20_L001... Success. Processing junction overhangs for Sample 4654-S136_S40_L001... Success. Processing junction overhangs for Sample 4654-S114_S18_L001... Success. Processing junction overhangs for Sample 4654-S134_S38_L001... Success. Processing junction overhangs for Sample 4654-S115_S19_L001... Success. Processing junction overhangs for Sample 4654-S120_S24_L001... Success. Processing junction overhangs for Sample 4654-S118_S22_L001... Success. sort: write failed: /tmp/sortyDi2zy: No space left on device sort: write failed: /tmp/sortW6Z6Pdsort: write failed: /tmp/sort4J3w93: No space left on device : No space left on device 4654-S113_S17_L001 4654-S114_S18_L001 4654-S115_S19_L001 cp: cannot stat '4654-S116_S20_L001_junction_counts_combined_intron_retention_event_list.txt': No such file or directory

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[DadongZ]

Thank you very much! It solved the issue.

[DadongZ]

Why didn't I see a JUM_diff/ directory after run the JUM_A.sh? Instead I got a new directory of temp_JUM_A_run?

[qqwang-berkeley]

Could you send me:

1) The complete report after you ran JUM_A.sh (start with

Sample names are:

4654-S113_S17_L001 4654-S114_S18_L001 4654-S115_S19_L001 4654-S116_S20_L001 4654-S117_S21_L001 4654-S118_S22_L001 4654-S119_S23_L001 4654-S120_S24_L001

etc.

2) the results of running

ls -l -t

in your current directory as well as the directory temp_JUM_A_run

This is for me to check the temporary files generated by time

On Tue, Apr 30, 2019 at 12:08 PM DadongZhang notifications@github.com wrote:

Why did I see a JUM_diff/ directory after run the JUM_A.sh? Instead I got a new directory of temp_JUM_A_run?

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[DadongZ]

The current directory only have two folders:

drwxr-sr-x  1 root dz33     5274 Jul 25  2018 JUM_2.0.2/
drwxrws---+ 1 dz33 dcistat 80972 Apr 30 15:25 temp_JUM_A_run/

In the temp_JUM_A_run:

-rw-rw----  1 dz33 dcistat     1520989 Apr 30 15:01 4654-S136_S40_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      639706 Apr 30 15:01 4654-S136_S40_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1519416 Apr 30 15:00 4654-S135_S39_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      639540 Apr 30 15:00 4654-S135_S39_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1521552 Apr 30 15:00 4654-S134_S38_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      640278 Apr 30 15:00 4654-S134_S38_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517922 Apr 30 15:00 4654-S133_S37_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      639030 Apr 30 15:00 4654-S133_S37_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517723 Apr 30 15:00 4654-S132_S36_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      637953 Apr 30 15:00 4654-S132_S36_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1516057 Apr 30 15:00 4654-S131_S35_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638359 Apr 30 15:00 4654-S131_S35_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1519173 Apr 30 15:00 4654-S130_S34_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638821 Apr 30 15:00 4654-S130_S34_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517609 Apr 30 15:00 4654-S129_S33_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638594 Apr 30 15:00 4654-S129_S33_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1519245 Apr 30 15:00 4654-S120_S24_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638435 Apr 30 15:00 4654-S120_S24_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517849 Apr 30 15:00 4654-S119_S23_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      637961 Apr 30 15:00 4654-S119_S23_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1520072 Apr 30 15:00 4654-S118_S22_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638886 Apr 30 15:00 4654-S118_S22_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1516490 Apr 30 15:00 4654-S117_S21_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      636874 Apr 30 15:00 4654-S117_S21_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1518621 Apr 30 15:00 4654-S116_S20_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638582 Apr 30 15:00 4654-S116_S20_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1519817 Apr 30 15:00 4654-S115_S19_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      638533 Apr 30 15:00 4654-S115_S19_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517956 Apr 30 15:00 4654-S114_S18_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      637339 Apr 30 15:00 4654-S114_S18_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     1517271 Apr 30 15:00 4654-S113_S17_L001_combined_count.txt
-rw-rw----  1 dz33 dcistat      636816 Apr 30 15:00 4654-S113_S17_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt
-rw-rw----  1 dz33 dcistat     8395362 Apr 30 15:00 combined_AS_JUM.gff
-rw-rw----  1 dz33 dcistat     3607998 Apr 30 15:00 output_intron_retention_splicing_event_JUM_annotation.gff
-rw-rw----  1 dz33 dcistat      453341 Apr 30 15:00 output_intron_retention_splicing_event_second_processing_for_JUM_reference_building.txt
-rw-rw----  1 dz33 dcistat      964882 Apr 30 15:00 output_intron_retention_splicing_event_first_processing_for_JUM_reference_building.txt
-rw-rw----  1 dz33 dcistat      906682 Apr 30 15:00 JUM_intron_retention_splicing_event.txt
-rw-rw----  1 dz33 dcistat      264496 Apr 30 15:00 All_junction_counts_intron_retention_in_all_samples_sorted_list.txt
drwxrws---+ 1 dz33 dcistat        1334 Apr 30 15:00 con2_2/
drwxrws---+ 1 dz33 dcistat        1334 Apr 30 15:00 con1_2/
-rw-rw----  1 dz33 dcistat    32678095 Apr 30 15:00 4654-S136_S40_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat      749788 Apr 30 15:00 4654-S136_S40_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2970 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10959241 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      368274 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10747868 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      378544 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10970986 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32652789 Apr 30 15:00 4654-S135_S39_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat     1113765 Apr 30 15:00 4654-S135_S39_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        3123 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10948889 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      547685 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10737981 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      562957 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10965919 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32695112 Apr 30 15:00 4654-S134_S38_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat     1156242 Apr 30 15:00 4654-S134_S38_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        3489 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10961268 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      568451 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10754991 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      584302 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10978853 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32606746 Apr 30 15:00 4654-S133_S37_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat      778864 Apr 30 15:00 4654-S133_S37_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2933 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10936158 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      382631 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10722134 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      393300 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10948454 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32628928 Apr 30 15:00 4654-S132_S36_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat      402324 Apr 30 15:00 4654-S132_S36_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2459 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10947305 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      197183 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10727387 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      202682 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10954236 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32558578 Apr 30 15:00 4654-S131_S35_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat      747794 Apr 30 15:00 4654-S131_S35_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2420 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10921619 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      367563 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10703558 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
-rw-rw----  1 dz33 dcistat      377811 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt
-rw-rw----  1 dz33 dcistat    10933401 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt
-rw-rw----  1 dz33 dcistat    32637469 Apr 30 14:59 4654-S130_S34_L001_junction_counts_combined_intron_retention_event.txt
-rw-rw----  1 dz33 dcistat      450176 Apr 30 14:59 4654-S130_S34_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        3015 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10948459 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      220506 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
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-rw-rw----  1 dz33 dcistat        2199 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
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-rw-rw----  1 dz33 dcistat        2750 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10940261 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
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-rw-rw----  1 dz33 dcistat      649286 Apr 30 14:59 4654-S115_S19_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2790 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10962172 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      318803 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
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-rw-rw----  1 dz33 dcistat      325691 Apr 30 14:59 4654-S114_S18_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2676 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10954526 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      159287 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10740405 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
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-rw-rw----  1 dz33 dcistat      300408 Apr 30 14:59 4654-S113_S17_L001_junction_counts_combined_intron_retention_event_list.txt
-rw-rw----  1 dz33 dcistat        2612 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt
-rw-rw----  1 dz33 dcistat    10948495 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt
-rw-rw----  1 dz33 dcistat      146851 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt
-rw-rw----  1 dz33 dcistat    10727842 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt
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-rw-rw----  1 dz33 dcistat      245413 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron2_count_table
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-rw-rw----  1 dz33 dcistat         489 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245359 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat      245402 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat           0 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245395 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat      245348 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron2_count_table
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-rw-rw----  1 dz33 dcistat           0 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245341 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245403 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat         767 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         767 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245391 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat          71 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245348 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron1_count_table
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-rw-rw----  1 dz33 dcistat     9126749 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat     8541050 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat     8264528 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat          55 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat      245397 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat         906 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245342 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245386 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat         346 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat     6469808 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat      245332 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245389 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat        1667 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat        1667 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245334 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat      245389 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat         622 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         622 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245391 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat      245385 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat         628 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         628 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat         489 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         489 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245331 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245399 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat      245335 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245337 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron1_count_table
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-rw-rw----  1 dz33 dcistat          55 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat      245394 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat        1455 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         695 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         695 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat     5457869 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat      245389 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat        1455 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat     5201721 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat      245345 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat     5192845 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat     5166628 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron1_chr_coor.txt
-rw-rw----  1 dz33 dcistat         279 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat         279 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_edited.txt
-rw-rw----  1 dz33 dcistat      245335 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245339 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron1_count_table
-rw-rw----  1 dz33 dcistat      245383 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron_count_table
-rw-rw----  1 dz33 dcistat         555 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron2_count_table
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-rw-rw----  1 dz33 dcistat          54 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron2_count_table
-rw-rw----  1 dz33 dcistat      245384 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron_count_table
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-rw-rw----  1 dz33 dcistat      245329 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron1_count_table
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-rw-rw----  1 dz33 dcistat      245330 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron1_count_table
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-rw-rw----  1 dz33 dcistat     4493299 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_long_intron_count_table
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-rw-rw----  1 dz33 dcistat      782020 Apr 30 14:41 4654-S135_S39_L001Aligned.out_intersect_short_intron2.txt
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-rw-rw----  1 dz33 dcistat      914563 Apr 30 14:41 4654-S132_S36_L001Aligned.out_intersect_short_intron2.txt
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-rw-rw----  1 dz33 dcistat      547997 Apr 30 14:40 4654-S117_S21_L001Aligned.out_intersect_short_intron2.txt
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-rw-rw----  1 dz33 dcistat  8320148045 Apr 30 14:39 4654-S118_S22_L001Aligned.out.sorted.bed
-rw-rw----  1 dz33 dcistat   262649386 Apr 30 14:39 4654-S115_S19_L001Aligned.out_intersect_long_intron.txt
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-rw-rw----  1 dz33 dcistat      355198 Apr 30 14:39 4654-S129_S33_L001Aligned.out_intersect_short_intron2.txt
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-rw-rw----  1 dz33 dcistat  8282440120 Apr 30 14:39 4654-S134_S38_L001Aligned.out.sorted.bed
-rw-rw----  1 dz33 dcistat   282121376 Apr 30 14:39 4654-S116_S20_L001Aligned.out_intersect_long_intron.txt
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-rw-rw----  1 dz33 dcistat     3984429 Apr 30 14:37 4654-S131_S35_L001Aligned.out_intersect_short_intron1.txt
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-rw-rw----  1 dz33 dcistat  6712207688 Apr 30 14:34 4654-S116_S20_L001Aligned.out.bed
-rw-rw----  1 dz33 dcistat  6424939940 Apr 30 14:34 4654-S130_S34_L001Aligned.out.bed
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-rw-rw----  1 dz33 dcistat      601554 Apr 30 14:26 output_short_intron_1_adjusted_range_sorted.bed
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-rw-rw----  1 dz33 dcistat         242 Apr 30 14:26 output_short_intron2_sorted.gff
-rw-rw----  1 dz33 dcistat     1109527 Apr 30 14:26 output_short_intron1_sorted.gff
-rw-rw----  1 dz33 dcistat         242 Apr 30 14:26 output_short_intron2.gff
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-rw-rw----  1 dz33 dcistat     5827690 Apr 30 13:23 UNION_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples_formatted_with_junction_length.txt
-rw-rw----  1 dz33 dcistat     5250368 Apr 30 13:23 UNION_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples.txt
-rw-rw----  1 dz33 dcistat     5250368 Apr 30 13:23 UNION_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples_formatted.txt
-rw-rw----  1 dz33 dcistat     4945406 Apr 30 13:23 condition2_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples_formatted.txt
-rw-rw----  1 dz33 dcistat     5045519 Apr 30 13:23 condition1_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples_formatted.txt
-rw-rw----  1 dz33 dcistat    14287462 Apr 30 13:23 4654-S136_S40_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    14133881 Apr 30 13:23 4654-S135_S39_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    14851371 Apr 30 13:23 4654-S134_S38_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13638330 Apr 30 13:23 4654-S133_S37_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13776279 Apr 30 13:23 4654-S132_S36_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13143631 Apr 30 13:23 4654-S131_S35_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13386972 Apr 30 13:23 4654-S130_S34_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13414289 Apr 30 13:23 4654-S129_S33_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13077354 Apr 30 13:23 4654-S120_S24_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13210765 Apr 30 13:23 4654-S119_S23_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    14424763 Apr 30 13:23 4654-S118_S22_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    12842694 Apr 30 13:23 4654-S117_S21_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    12709165 Apr 30 13:23 4654-S116_S20_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    13672105 Apr 30 13:23 4654-S115_S19_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    12855180 Apr 30 13:23 4654-S114_S18_L001_junction_counts.txt
-rw-rw----  1 dz33 dcistat    12602341 Apr 30 13:23 4654-S113_S17_L001_junction_counts.txt
drwxrws---+ 1 dz33 dcistat        2578 Apr 30 13:23 con2_1/
drwxrws---+ 1 dz33 dcistat        2578 Apr 30 13:23 con1_1/
-rw-rw----  1 dz33 dcistat    35339846 Apr 30 13:22 UNION_junc_coor_with_junction_ID.txt
-rw-rw----  1 dz33 dcistat    21929015 Apr 30 13:22 UNION_junc_coor.txt
-rw-rw----  1 dz33 dcistat     7801660 Apr 30 13:21 4654-S136_S40_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    11332346 Apr 30 13:21 4654-S136_S40_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7723898 Apr 30 13:21 4654-S135_S39_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    11207007 Apr 30 13:21 4654-S135_S39_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     8110830 Apr 30 13:21 4654-S134_S38_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    11779048 Apr 30 13:21 4654-S134_S38_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7455922 Apr 30 13:21 4654-S133_S37_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10812853 Apr 30 13:21 4654-S133_S37_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7524849 Apr 30 13:21 4654-S132_S36_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10925660 Apr 30 13:21 4654-S132_S36_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7189471 Apr 30 13:21 4654-S131_S35_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10418258 Apr 30 13:21 4654-S131_S35_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7309451 Apr 30 13:21 4654-S130_S34_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10617351 Apr 30 13:21 4654-S130_S34_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7333068 Apr 30 13:21 4654-S129_S33_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10635732 Apr 30 13:21 4654-S129_S33_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7130588 Apr 30 13:21 4654-S120_S24_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10375315 Apr 30 13:21 4654-S120_S24_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7209406 Apr 30 13:21 4654-S119_S23_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10479535 Apr 30 13:21 4654-S119_S23_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7867235 Apr 30 13:21 4654-S118_S22_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    11443433 Apr 30 13:21 4654-S118_S22_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7012941 Apr 30 13:21 4654-S117_S21_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10184266 Apr 30 13:21 4654-S117_S21_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     6938003 Apr 30 13:21 4654-S116_S20_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10079900 Apr 30 13:21 4654-S116_S20_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7456413 Apr 30 13:21 4654-S115_S19_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10847415 Apr 30 13:21 4654-S115_S19_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     7008461 Apr 30 13:21 4654-S114_S18_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat    10199081 Apr 30 13:21 4654-S114_S18_L001SJ.out.tab_strand_symbol_scaled
-rw-rw----  1 dz33 dcistat     6870004 Apr 30 13:21 4654-S113_S17_L001_SJ_coor.txt
-rw-rw----  1 dz33 dcistat     9998214 Apr 30 13:21 4654-S113_S17_L001SJ.out.tab_strand_symbol_scaled
-rwxr-xr-x  1 dz33 dcistat         662 Apr 29 15:18 jum.sh*
-rw-rw----  1 root dcistat 44800718373 Apr 24 17:38 4654-S136_S40_L001Aligned.out.sam
-rw-rw----  1 root dcistat 40017868701 Apr 24 17:24 4654-S135_S39_L001Aligned.out.sam
-rw-rw----  1 root dcistat 48509167729 Apr 24 17:12 4654-S134_S38_L001Aligned.out.sam
-rw-rw----  1 root dcistat 38530668414 Apr 24 16:57 4654-S133_S37_L001Aligned.out.sam
-rw-rw----  1 root dcistat 37357452106 Apr 24 16:46 4654-S132_S36_L001Aligned.out.sam
-rw-rw----  1 root dcistat 33049889873 Apr 24 16:35 4654-S131_S35_L001Aligned.out.sam
-rw-rw----  1 root dcistat 37588895638 Apr 24 16:25 4654-S130_S34_L001Aligned.out.sam
-rw-rw----  1 root dcistat 34624631664 Apr 24 16:14 4654-S129_S33_L001Aligned.out.sam
-rw-rw----  1 root dcistat 44326343980 Apr 24 16:04 4654-S120_S24_L001Aligned.out.sam
-rw-rw----  1 root dcistat 39788177797 Apr 24 15:50 4654-S119_S23_L001Aligned.out.sam
-rw-rw----  1 root dcistat 49443101528 Apr 24 15:39 4654-S118_S22_L001Aligned.out.sam
-rw-rw----  1 root dcistat 37213113256 Apr 24 15:24 4654-S117_S21_L001Aligned.out.sam
-rw-rw----  1 root dcistat 39127466671 Apr 24 15:12 4654-S116_S20_L001Aligned.out.sam
-rw-rw----  1 root dcistat 43040847354 Apr 24 15:00 4654-S115_S19_L001Aligned.out.sam
-rw-rw----  1 root dcistat 42384156572 Apr 24 14:47 4654-S114_S18_L001Aligned.out.sam
-rw-rw----  1 root dcistat 40327211185 Apr 24 14:34 4654-S113_S17_L001Aligned.out.sam
-rwxr-x---  1 root dcistat         439 Apr 24 14:21 bamtosam.sh*
-rw-rw----  1 root dcistat    11332346 Apr  5 14:33 4654-S136_S40_L001SJ.out.tab
-rw-rw----  1 root dcistat  6049884142 Apr  5 14:33 4654-S136_S40_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    11207007 Apr  5 14:32 4654-S135_S39_L001SJ.out.tab
-rw-rw----  1 root dcistat  5635195742 Apr  5 14:32 4654-S135_S39_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    11779048 Apr  5 14:31 4654-S134_S38_L001SJ.out.tab
-rw-rw----  1 root dcistat  6657829883 Apr  5 14:31 4654-S134_S38_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10812853 Apr  5 14:31 4654-S133_S37_L001SJ.out.tab
-rw-rw----  1 root dcistat  5253935326 Apr  5 14:31 4654-S133_S37_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10925660 Apr  5 14:30 4654-S132_S36_L001SJ.out.tab
-rw-rw----  1 root dcistat  5040146315 Apr  5 14:30 4654-S132_S36_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10418258 Apr  5 14:29 4654-S131_S35_L001SJ.out.tab
-rw-rw----  1 root dcistat  4567350036 Apr  5 14:29 4654-S131_S35_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10617351 Apr  5 14:28 4654-S130_S34_L001SJ.out.tab
-rw-rw----  1 root dcistat  5163908447 Apr  5 14:28 4654-S130_S34_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10635732 Apr  5 14:27 4654-S129_S33_L001SJ.out.tab
-rw-rw----  1 root dcistat  4638363330 Apr  5 14:27 4654-S129_S33_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10375315 Apr  5 14:26 4654-S120_S24_L001SJ.out.tab
-rw-rw----  1 root dcistat  6041356332 Apr  5 14:26 4654-S120_S24_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10479535 Apr  5 14:25 4654-S119_S23_L001SJ.out.tab
-rw-rw----  1 root dcistat  5372589955 Apr  5 14:25 4654-S119_S23_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    11443433 Apr  5 14:24 4654-S118_S22_L001SJ.out.tab
-rw-rw----  1 root dcistat  6708048660 Apr  5 14:24 4654-S118_S22_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10184266 Apr  5 14:23 4654-S117_S21_L001SJ.out.tab
-rw-rw----  1 root dcistat  4991508012 Apr  5 14:23 4654-S117_S21_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10079900 Apr  5 14:22 4654-S116_S20_L001SJ.out.tab
-rw-rw----  1 root dcistat  5353504888 Apr  5 14:22 4654-S116_S20_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10847415 Apr  5 14:21 4654-S115_S19_L001SJ.out.tab
-rw-rw----  1 root dcistat  5832351256 Apr  5 14:21 4654-S115_S19_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat    10199081 Apr  5 14:20 4654-S114_S18_L001SJ.out.tab
-rw-rw----  1 root dcistat  5734624045 Apr  5 14:20 4654-S114_S18_L001Aligned.out_sorted.bam
-rw-rw----  1 root dcistat     9998214 Apr  5 14:19 4654-S113_S17_L001SJ.out.tab
-rw-rw----  1 root dcistat  5534011228 Apr  5 14:19 4654-S113_S17_L001Aligned.out_sorted.bam

[qqwang-berkeley]

Looks to me JUM_A.sh finished successfully. There might be some folder re-arrangement issues.

Could you send me the complete report by running JUM_A.sh? it is something like:

Sample names are: 4654-S113_S17_L001 4654-S114_S18_L001 4654-S115_S19_L001 4654-S116_S20_L001 4654-S117_S21_L001 4654-S118_S22_L001 4654-S119_S23_L001 4654-S120_S24_L001 4654-S129_S33_L001 4654-S130_S34_L001 4654-S131_S35_L001 4654-S132_S36_L001 4654-S133_S37_L001 4654-S134_S38_L001 4654-S135_S39_L001 4654-S136_S40_L001 8 input samples to consider under the current condition 8 input samples to consider under the current condition Preparing for intron retention AS events analyses... Processing junction overhangs for Sample 4654-S131_S35_L001... Success. Processing junction overhangs for Sample 4654-S135_S39_L001... Success. Processing junction overhangs for Sample 4654-S129_S33_L001... Success. Processing junction overhangs for Sample 4654-S133_S37_L001... Success. Processing junction overhangs for Sample 4654-S132_S36_L001... Success. Processing junction overhangs for Sample 4654-S130_S34_L001... Success. Processing junction overhangs for Sample 4654-S119_S23_L001... Success. Processing junction overhangs for Sample 4654-S117_S21_L001... Success. Processing junction overhangs for Sample 4654-S113_S17_L001... Success. Processing junction overhangs for Sample 4654-S116_S20_L001... Success. Processing junction overhangs for Sample 4654-S136_S40_L001... Success. Processing junction overhangs for Sample 4654-S114_S18_L001... Success. Processing junction overhangs for Sample 4654-S134_S38_L001... Success. Processing junction overhangs for Sample 4654-S115_S19_L001... Success. Processing junction overhangs for Sample 4654-S120_S24_L001... Success. Processing junction overhangs for Sample 4654-S118_S22_L001... Success.

On Tue, Apr 30, 2019 at 12:31 PM DadongZhang notifications@github.com wrote:

The current directory only have two folders:

drwxr-sr-x 1 root dz33 5274 Jul 25 2018 JUM_2.0.2/ drwxrws---+ 1 dz33 dcistat 80972 Apr 30 15:25 temp_JUM_A_run/

In the temp_JUM_A_run:

-rw-rw---- 1 dz33 dcistat 1520989 Apr 30 15:01 4654-S136_S40_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 639706 Apr 30 15:01 4654-S136_S40_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1519416 Apr 30 15:00 4654-S135_S39_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 639540 Apr 30 15:00 4654-S135_S39_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1521552 Apr 30 15:00 4654-S134_S38_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 640278 Apr 30 15:00 4654-S134_S38_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517922 Apr 30 15:00 4654-S133_S37_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 639030 Apr 30 15:00 4654-S133_S37_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517723 Apr 30 15:00 4654-S132_S36_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 637953 Apr 30 15:00 4654-S132_S36_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1516057 Apr 30 15:00 4654-S131_S35_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638359 Apr 30 15:00 4654-S131_S35_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1519173 Apr 30 15:00 4654-S130_S34_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638821 Apr 30 15:00 4654-S130_S34_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517609 Apr 30 15:00 4654-S129_S33_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638594 Apr 30 15:00 4654-S129_S33_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1519245 Apr 30 15:00 4654-S120_S24_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638435 Apr 30 15:00 4654-S120_S24_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517849 Apr 30 15:00 4654-S119_S23_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 637961 Apr 30 15:00 4654-S119_S23_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1520072 Apr 30 15:00 4654-S118_S22_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638886 Apr 30 15:00 4654-S118_S22_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1516490 Apr 30 15:00 4654-S117_S21_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 636874 Apr 30 15:00 4654-S117_S21_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1518621 Apr 30 15:00 4654-S116_S20_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638582 Apr 30 15:00 4654-S116_S20_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1519817 Apr 30 15:00 4654-S115_S19_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 638533 Apr 30 15:00 4654-S115_S19_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517956 Apr 30 15:00 4654-S114_S18_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 637339 Apr 30 15:00 4654-S114_S18_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 1517271 Apr 30 15:00 4654-S113_S17_L001_combined_count.txt -rw-rw---- 1 dz33 dcistat 636816 Apr 30 15:00 4654-S113_S17_L001_junction_counts_intron_retention_counts_exist_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 8395362 Apr 30 15:00 combined_AS_JUM.gff -rw-rw---- 1 dz33 dcistat 3607998 Apr 30 15:00 output_intron_retention_splicing_event_JUM_annotation.gff -rw-rw---- 1 dz33 dcistat 453341 Apr 30 15:00 output_intron_retention_splicing_event_second_processing_for_JUM_reference_building.txt -rw-rw---- 1 dz33 dcistat 964882 Apr 30 15:00 output_intron_retention_splicing_event_first_processing_for_JUM_reference_building.txt -rw-rw---- 1 dz33 dcistat 906682 Apr 30 15:00 JUM_intron_retention_splicing_event.txt -rw-rw---- 1 dz33 dcistat 264496 Apr 30 15:00 All_junction_counts_intron_retention_in_all_samples_sorted_list.txt drwxrws---+ 1 dz33 dcistat 1334 Apr 30 15:00 con2_2/ drwxrws---+ 1 dz33 dcistat 1334 Apr 30 15:00 con1_2/ -rw-rw---- 1 dz33 dcistat 32678095 Apr 30 15:00 4654-S136_S40_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 749788 Apr 30 15:00 4654-S136_S40_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2970 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10959241 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 368274 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10747868 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 378544 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10970986 Apr 30 15:00 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32652789 Apr 30 15:00 4654-S135_S39_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 1113765 Apr 30 15:00 4654-S135_S39_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 3123 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10948889 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 547685 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10737981 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 562957 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10965919 Apr 30 15:00 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32695112 Apr 30 15:00 4654-S134_S38_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 1156242 Apr 30 15:00 4654-S134_S38_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 3489 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10961268 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 568451 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10754991 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 584302 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10978853 Apr 30 15:00 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32606746 Apr 30 15:00 4654-S133_S37_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 778864 Apr 30 15:00 4654-S133_S37_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2933 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10936158 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 382631 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10722134 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 393300 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10948454 Apr 30 15:00 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32628928 Apr 30 15:00 4654-S132_S36_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 402324 Apr 30 15:00 4654-S132_S36_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2459 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10947305 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 197183 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10727387 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 202682 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10954236 Apr 30 15:00 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32558578 Apr 30 15:00 4654-S131_S35_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 747794 Apr 30 15:00 4654-S131_S35_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2420 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10921619 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 367563 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10703558 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 377811 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10933401 Apr 30 15:00 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32637469 Apr 30 14:59 4654-S130_S34_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 450176 Apr 30 14:59 4654-S130_S34_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 3015 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10948459 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 220506 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10732862 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 226655 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10956148 Apr 30 14:59 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32589260 Apr 30 14:59 4654-S129_S33_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 513055 Apr 30 14:59 4654-S129_S33_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2347 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10932973 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 251843 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10714802 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 258865 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10941485 Apr 30 14:59 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32667778 Apr 30 14:59 4654-S120_S24_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 574358 Apr 30 14:59 4654-S120_S24_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2680 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10956907 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 281909 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10744718 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 289769 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10966153 Apr 30 14:59 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32639366 Apr 30 14:59 4654-S119_S23_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 697235 Apr 30 14:59 4654-S119_S23_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2567 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10947801 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 342558 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10732612 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 352110 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10958953 Apr 30 14:59 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32703452 Apr 30 14:59 4654-S118_S22_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 836320 Apr 30 14:59 4654-S118_S22_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2976 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10968725 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 410943 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10753042 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 422401 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10981685 Apr 30 14:59 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32592670 Apr 30 14:59 4654-S117_S21_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 250396 Apr 30 14:59 4654-S117_S21_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2199 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10935948 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 122392 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10715692 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 125805 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10941030 Apr 30 14:59 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32612894 Apr 30 14:59 4654-S116_S20_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 446522 Apr 30 14:59 4654-S116_S20_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2750 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10940261 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 218835 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10724741 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 224937 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10947892 Apr 30 14:59 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32684961 Apr 30 14:59 4654-S115_S19_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 649286 Apr 30 14:59 4654-S115_S19_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2790 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10962172 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 318803 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10750334 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 327693 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10972455 Apr 30 14:59 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32655388 Apr 30 14:59 4654-S114_S18_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 325691 Apr 30 14:59 4654-S114_S18_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2676 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10954526 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 159287 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10740405 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 163728 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10960457 Apr 30 14:59 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 32630555 Apr 30 14:59 4654-S113_S17_L001_junction_counts_combined_intron_retention_event.txt -rw-rw---- 1 dz33 dcistat 300408 Apr 30 14:59 4654-S113_S17_L001_junction_counts_combined_intron_retention_event_list.txt -rw-rw---- 1 dz33 dcistat 2612 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention_list.txt -rw-rw---- 1 dz33 dcistat 10948495 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_short_intron_retention.txt -rw-rw---- 1 dz33 dcistat 146851 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count_list.txt -rw-rw---- 1 dz33 dcistat 10727842 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_left_count.txt -rw-rw---- 1 dz33 dcistat 150945 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count_list.txt -rw-rw---- 1 dz33 dcistat 10954218 Apr 30 14:59 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_long_intron_retention_right_count.txt -rw-rw---- 1 dz33 dcistat 245413 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 489 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 489 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245359 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 245402 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245395 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 10234484 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 245348 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245341 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245403 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 55 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 767 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 767 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245391 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 71 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 71 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245348 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245337 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 9125091 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 9126749 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 8541050 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 8264528 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 55 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 245397 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 906 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 906 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245342 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245386 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 346 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 346 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 6469808 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 245332 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245389 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 55 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 1667 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 1667 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245334 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 245389 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 622 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 622 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245391 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 245385 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 628 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 628 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 489 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 489 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245331 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245399 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 245335 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245337 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 5611593 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 55 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 245394 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 1455 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 695 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 695 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 5457869 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 245389 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 1455 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 5201721 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 245345 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 5192845 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 5166628 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 279 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 279 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245335 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245339 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 245383 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 555 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 555 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 54 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron2_count_table -rw-rw---- 1 dz33 dcistat 245384 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron_count_table -rw-rw---- 1 dz33 dcistat 278 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw---- 1 dz33 dcistat 245329 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 278 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron2_edited.txt -rw-rw---- 1 dz33 dcistat 245330 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron1_count_table -rw-rw---- 1 dz33 dcistat 4427553 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4393955 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4420085 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4276204 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 3984429 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_short_intron1_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4504316 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4484959 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4491223 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4489955 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4483245 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4477629 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 319090414 Apr 30 14:59 4654-S134_S38_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4493299 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4485049 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4484697 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 282121376 Apr 30 14:59 4654-S116_S20_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 283402474 Apr 30 14:59 4654-S133_S37_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4491375 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 282429397 Apr 30 14:59 4654-S120_S24_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4486577 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4499087 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 253937508 Apr 30 14:59 4654-S117_S21_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 260623766 Apr 30 14:59 4654-S129_S33_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4488803 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 4490206 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 274966973 Apr 30 14:59 4654-S136_S40_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 265785227 Apr 30 14:59 4654-S130_S34_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4477873 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 258443644 Apr 30 14:59 4654-S114_S18_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 262649386 Apr 30 14:59 4654-S115_S19_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 248849286 Apr 30 14:59 4654-S131_S35_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 267716734 Apr 30 14:59 4654-S135_S39_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 4479945 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_long_intron_count_table -rw-rw---- 1 dz33 dcistat 243546836 Apr 30 14:59 4654-S119_S23_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 242298067 Apr 30 14:59 4654-S118_S22_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 221571447 Apr 30 14:59 4654-S113_S17_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 217525085 Apr 30 14:59 4654-S132_S36_L001Aligned.out_intersect_long_intron_chr_coor.txt -rw-rw---- 1 dz33 dcistat 977149031 Apr 30 14:58 4654-S118_S22_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 981508386 Apr 30 14:58 4654-S134_S38_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 868354829 Apr 30 14:57 4654-S136_S40_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 816751556 Apr 30 14:57 4654-S120_S24_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 843754255 Apr 30 14:57 4654-S115_S19_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 755637096 Apr 30 14:56 4654-S114_S18_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 921396167 Apr 30 14:56 4654-S135_S39_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 815050913 Apr 30 14:56 4654-S119_S23_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 726474096 Apr 30 14:56 4654-S113_S17_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 789399681 Apr 30 14:55 4654-S133_S37_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 698807685 Apr 30 14:55 4654-S116_S20_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 750933820 Apr 30 14:55 4654-S132_S36_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 734303622 Apr 30 14:55 4654-S130_S34_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 642384327 Apr 30 14:55 4654-S117_S21_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 688568272 Apr 30 14:54 4654-S129_S33_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 728350640 Apr 30 14:54 4654-S131_S35_L001Aligned.out_coverage.bed -rw-rw---- 1 dz33 dcistat 1145443 Apr 30 14:44 4654-S118_S22_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 1283360 Apr 30 14:44 4654-S134_S38_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 4420085 Apr 30 14:43 4654-S118_S22_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 10234484 Apr 30 14:42 4654-S134_S38_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 1775997 Apr 30 14:42 4654-S120_S24_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 881983 Apr 30 14:42 4654-S114_S18_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 360606 Apr 30 14:42 4654-S136_S40_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 3020986 Apr 30 14:42 4654-S115_S19_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 1396661 Apr 30 14:41 4654-S119_S23_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 1085346 Apr 30 14:41 4654-S116_S20_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 242298067 Apr 30 14:41 4654-S118_S22_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 8264528 Apr 30 14:41 4654-S114_S18_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 5166628 Apr 30 14:41 4654-S120_S24_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 9125091 Apr 30 14:41 4654-S136_S40_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 782020 Apr 30 14:41 4654-S135_S39_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 319090414 Apr 30 14:41 4654-S134_S38_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 914563 Apr 30 14:41 4654-S132_S36_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 985866 Apr 30 14:41 4654-S113_S17_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 4393955 Apr 30 14:41 4654-S115_S19_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 547997 Apr 30 14:40 4654-S117_S21_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 5457869 Apr 30 14:40 4654-S119_S23_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 6469808 Apr 30 14:40 4654-S116_S20_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 2277865 Apr 30 14:40 4654-S130_S34_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 300971 Apr 30 14:40 4654-S133_S37_L001Aligned.out_intersect_short_intron2.txt -rw-rw---- 1 dz33 dcistat 8541050 Apr 30 14:40 4654-S135_S39_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 5611593 Apr 30 14:40 4654-S132_S36_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 258443644 Apr 30 14:40 4654-S114_S18_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 282429397 Apr 30 14:39 4654-S120_S24_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 5201721 Apr 30 14:39 4654-S117_S21_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 5192845 Apr 30 14:39 4654-S113_S17_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 274966973 Apr 30 14:39 4654-S136_S40_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 8320148045 Apr 30 14:39 4654-S118_S22_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 262649386 Apr 30 14:39 4654-S115_S19_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 4427553 Apr 30 14:39 4654-S130_S34_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 355198 Apr 30 14:39 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14:37 4654-S129_S33_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 6830583214 Apr 30 14:37 4654-S135_S39_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6358113222 Apr 30 14:37 4654-S132_S36_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 8320148045 Apr 30 14:37 4654-S118_S22_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6367323710 Apr 30 14:36 4654-S117_S21_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6826123464 Apr 30 14:36 4654-S113_S17_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 8282440120 Apr 30 14:36 4654-S134_S38_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 248849286 Apr 30 14:36 4654-S131_S35_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 6424939940 Apr 30 14:36 4654-S130_S34_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6627519297 Apr 30 14:36 4654-S133_S37_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 7559385270 Apr 30 14:35 4654-S120_S24_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 7253058038 Apr 30 14:35 4654-S114_S18_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 7319724917 Apr 30 14:35 4654-S115_S19_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 7639114190 Apr 30 14:35 4654-S136_S40_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6766989973 Apr 30 14:34 4654-S119_S23_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 5946496598 Apr 30 14:34 4654-S129_S33_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6712207688 Apr 30 14:34 4654-S116_S20_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6424939940 Apr 30 14:34 4654-S130_S34_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 5663072353 Apr 30 14:34 4654-S131_S35_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6367323710 Apr 30 14:34 4654-S117_S21_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6358113222 Apr 30 14:34 4654-S132_S36_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6830583214 Apr 30 14:34 4654-S135_S39_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 6826123464 Apr 30 14:34 4654-S113_S17_L001Aligned.out.bed 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4654-S120_S24_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4428011762 Apr 30 14:11 4654-S134_S38_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4512182889 Apr 30 14:11 4654-S115_S19_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4220049632 Apr 30 14:10 4654-S136_S40_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4351802416 Apr 30 14:10 4654-S113_S17_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4215364980 Apr 30 14:10 4654-S114_S18_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4112472427 Apr 30 14:10 4654-S116_S20_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3961906048 Apr 30 14:10 4654-S130_S34_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3937737013 Apr 30 14:10 4654-S119_S23_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3586447159 Apr 30 14:10 4654-S133_S37_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4052435446 Apr 30 14:09 4654-S117_S21_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3574339684 Apr 30 14:09 4654-S135_S39_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3801823714 Apr 30 14:08 4654-S132_S36_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3687795104 Apr 30 14:07 4654-S129_S33_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 3349515473 Apr 30 14:06 4654-S131_S35_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 21327186815 Apr 30 14:04 4654-S118_S22_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 20137871653 Apr 30 14:03 4654-S134_S38_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 21225166607 Apr 30 14:03 4654-S120_S24_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 19219766369 Apr 30 14:03 4654-S114_S18_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 16590219067 Apr 30 14:03 4654-S133_S37_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 19454476491 Apr 30 14:03 4654-S113_S17_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 19129057703 Apr 30 14:02 4654-S136_S40_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 18824919934 Apr 30 14:02 4654-S116_S20_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 20430744406 Apr 30 14:02 4654-S115_S19_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 2169 Apr 30 14:01 4654-S118_S22_L001_sam_header -rw-rw---- 1 dz33 dcistat 16139731965 Apr 30 14:00 4654-S135_S39_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 21327184646 Apr 30 14:00 4654-S118_S22_L001_temp1 -rw-rw---- 1 dz33 dcistat 18094441905 Apr 30 14:00 4654-S130_S34_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 17923689579 Apr 30 14:00 4654-S119_S23_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 18606217986 Apr 30 13:58 4654-S117_S21_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 2169 Apr 30 13:57 4654-S134_S38_L001_sam_header -rw-rw---- 1 dz33 dcistat 20137869484 Apr 30 13:57 4654-S134_S38_L001_temp1 -rw-rw---- 1 dz33 dcistat 2169 Apr 30 13:55 4654-S114_S18_L001_sam_header -rw-rw---- 1 dz33 dcistat 19219764200 Apr 30 13:55 4654-S114_S18_L001_temp1 -rw-rw---- 1 dz33 dcistat 2169 Apr 30 13:55 4654-S120_S24_L001_sam_header -rw-rw---- 1 dz33 dcistat 21225164438 Apr 30 13:55 4654-S120_S24_L001_temp1 -rw-rw---- 1 dz33 dcistat 17344840496 Apr 30 13:54 4654-S132_S36_L001_Aligned.out.spanning_junction_reads.sam -rw-rw---- 1 dz33 dcistat 2169 Apr 30 13:54 4654-S115_S19_L001_sam_header -rw-rw---- 1 dz33 dcistat 20430742237 Apr 30 13:54 4654-S115_S19_L001_temp1 -rw-rw---- 1 dz33 dcistat 2169 Apr 30 13:54 4654-S136_S40_L001_sam_header -rw-rw---- 1 d

[DadongZ]

I saw this message at the end "move JUM_2.0.2/ to temp_JUM_A_run/ permission denied" but if temp_JUM_A_run/ can be created why it isn't writable. I saw both directories I have rwx permissions.

[qqwang-berkeley]

I see what happened. I did not know that you put the JUM_2.0.2 program folder in the same directory where you run your analysis. It is best that in the directory you run JUM you only keep all the input files like sam/bam/SJ.out.tab files etc. You can move the JUM_2.0.2 to, say, your local path where you keep all your software tools.

The reason you saw the error is because JUM_2.0.2 is a directory... it is not compatible with the specific "moving" command in the last few lines of JUM_A.sh where it will move all files into temp_JUM_A_run (before creating the JUM_diff folder and re-arrange files for the next step).

This deny message stopped the last few lines of JUM_A.sh which does the file re-arrangement for you. You just need to do it yourself. Copy and paste the following command under your current directory (parent of temp_JUM_A_run). You should be all good to go.

mkdir JUM_diff;

mv temp_JUM_A_run/*combined_count.txt JUM_diff/

mv temp_JUM_A_run/combined_AS_JUM.gff JUM_diff/

mv temp_JUM_A_run/*Aligned.out_coverage.bed JUM_diff/

mv temp_JUM_A_run/*profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt JUM_diff/

mv temp_JUM_A_run/UNION_junc_coor_with_junction_ID_morethan"$threshold"_read_in_atleast"$file_num"_samples.txt JUM_diff/

mv temp_JUM_A_run/*Aligned.out.sam .

mv temp_JUM_A_run/Aligned.out_sorted.bam .

mv temp_JUM_A_run/*formatted.txt .

mv temp_JUM_A_run/*SJ.out.tab .

On Tue, Apr 30, 2019 at 12:54 PM DadongZhang notifications@github.com wrote:

I saw this message at the end "move JUM_2.0.2/ to temp_JUM_A_run/ permission denied" but if temp_JUM_A_run/ can be created why it isn't writable. I saw both directories I have rwx permissions.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/qqwang-berkeley/JUM/issues/21#issuecomment-488092111, or mute the thread https://github.com/notifications/unsubscribe-auth/AGJ6PW2ZXCCM23BCYXSMUOTPTCPXVANCNFSM4HHZCG5Q .

[DadongZ]

Thank you very much! Will try it and let you know.