Closed DadongZ closed 5 years ago
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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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).
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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Thank you very much! It solved the issue.
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
?
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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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
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drwxrws---+ 1 dz33 dcistat 2578 Apr 30 13:23 con2_1/
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-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
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 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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 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dz33 dcistat 4276204 Apr 30 14:38 4654-S129_S33_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 7253058038 Apr 30 14:38 4654-S114_S18_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 265785227 Apr 30 14:38 4654-S130_S34_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 7559385270 Apr 30 14:38 4654-S120_S24_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 283402474 Apr 30 14:37 4654-S133_S37_L001Aligned.out_intersect_long_intron.txt -rw-rw---- 1 dz33 dcistat 7639114190 Apr 30 14:37 4654-S136_S40_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 3984429 Apr 30 14:37 4654-S131_S35_L001Aligned.out_intersect_short_intron1.txt -rw-rw---- 1 dz33 dcistat 7319724917 Apr 30 14:37 4654-S115_S19_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6712207688 Apr 30 14:37 4654-S116_S20_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 6766989973 Apr 30 14:37 4654-S119_S23_L001Aligned.out.sorted.bed -rw-rw---- 1 dz33 dcistat 260623766 Apr 30 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 -rw-rw---- 1 dz33 dcistat 6627519297 Apr 30 14:33 4654-S133_S37_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 5946496598 Apr 30 14:33 4654-S129_S33_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 5663072353 Apr 30 14:33 4654-S131_S35_L001Aligned.out.bed -rw-rw---- 1 dz33 dcistat 131 Apr 30 14:26 output_short_intron_2_adjusted_range_sorted.bed -rw-rw---- 1 dz33 dcistat 601554 Apr 30 14:26 output_short_intron_1_adjusted_range_sorted.bed -rw-rw---- 1 dz33 dcistat 10246622 Apr 30 14:26 output_long_intron_adjusted_range_sorted.bed -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 -rw-rw---- 1 dz33 dcistat 1109527 Apr 30 14:26 output_short_intron1.gff -rw-rw---- 1 dz33 dcistat 18519156 Apr 30 14:26 output_long_intron_sorted.gff -rw-rw---- 1 dz33 dcistat 18519156 Apr 30 14:26 output_long_intron.gff -rw-rw---- 1 dz33 dcistat 1109769 Apr 30 14:26 output_short_intron.gff -rw-rw---- 1 dz33 dcistat 6797580 Apr 30 14:26 UNION_junc_coor_with_junction_ID_more_than_8_read_in_at_least_8_samples_formatted_with_junction_length_and_overhang_union_from_all_samples.txt -rw-rw---- 1 dz33 dcistat 7502557 Apr 30 14:26 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:26 4654-S118_S22_L001_trash_out -rw-rw---- 1 dz33 dcistat 6086330 Apr 30 14:26 4654-S118_S22_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11660513 Apr 30 14:26 profiled_4654-S118_S22_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7479352 Apr 30 14:26 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:26 4654-S120_S24_L001_trash_out -rw-rw---- 1 dz33 dcistat 6075256 Apr 30 14:26 4654-S120_S24_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10519534 Apr 30 14:26 profiled_4654-S120_S24_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7488721 Apr 30 14:25 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:25 4654-S115_S19_L001_trash_out -rw-rw---- 1 dz33 dcistat 6080105 Apr 30 14:25 4654-S115_S19_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11074831 Apr 30 14:25 profiled_4654-S115_S19_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7490268 Apr 30 14:25 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:25 4654-S134_S38_L001_trash_out -rw-rw---- 1 dz33 dcistat 6077993 Apr 30 14:25 4654-S134_S38_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 12137103 Apr 30 14:25 profiled_4654-S134_S38_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7483938 Apr 30 14:24 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:24 4654-S136_S40_L001_trash_out -rw-rw---- 1 dz33 dcistat 6077065 Apr 30 14:24 4654-S136_S40_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11718478 Apr 30 14:24 profiled_4654-S136_S40_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7462742 Apr 30 14:24 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:24 4654-S113_S17_L001_trash_out -rw-rw---- 1 dz33 dcistat 6068586 Apr 30 14:24 4654-S113_S17_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10201170 Apr 30 14:24 profiled_4654-S113_S17_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7471412 Apr 30 14:24 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:24 4654-S114_S18_L001_trash_out -rw-rw---- 1 dz33 dcistat 6072911 Apr 30 14:24 4654-S114_S18_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10479754 Apr 30 14:24 profiled_4654-S114_S18_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7446995 Apr 30 14:23 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:23 4654-S116_S20_L001_trash_out -rw-rw---- 1 dz33 dcistat 6059264 Apr 30 14:23 4654-S116_S20_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10290239 Apr 30 14:23 profiled_4654-S116_S20_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7436716 Apr 30 14:23 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:23 4654-S117_S21_L001_trash_out -rw-rw---- 1 dz33 dcistat 6055651 Apr 30 14:23 4654-S117_S21_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10237998 Apr 30 14:23 profiled_4654-S117_S21_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7458395 Apr 30 14:22 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:22 4654-S130_S34_L001_trash_out -rw-rw---- 1 dz33 dcistat 6065803 Apr 30 14:22 4654-S130_S34_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11400173 Apr 30 14:22 profiled_4654-S130_S34_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7465414 Apr 30 14:22 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:22 4654-S119_S23_L001_trash_out -rw-rw---- 1 dz33 dcistat 6067012 Apr 30 14:22 4654-S119_S23_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10589696 Apr 30 14:22 profiled_4654-S119_S23_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7439750 Apr 30 14:21 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:21 4654-S133_S37_L001_trash_out -rw-rw---- 1 dz33 dcistat 6053953 Apr 30 14:21 4654-S133_S37_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11048626 Apr 30 14:21 profiled_4654-S133_S37_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7465796 Apr 30 14:21 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 7454361 Apr 30 14:21 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:21 4654-S135_S39_L001_trash_out -rw-rw---- 1 dz33 dcistat 6065920 Apr 30 14:21 4654-S135_S39_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:21 4654-S132_S36_L001_trash_out -rw-rw---- 1 dz33 dcistat 6064471 Apr 30 14:21 4654-S132_S36_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 11657818 Apr 30 14:21 profiled_4654-S135_S39_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 11200094 Apr 30 14:21 profiled_4654-S132_S36_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 7428305 Apr 30 14:20 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:20 4654-S129_S33_L001_trash_out -rw-rw---- 1 dz33 dcistat 6050726 Apr 30 14:20 4654-S129_S33_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10890963 Apr 30 14:20 profiled_4654-S129_S33_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 5684198792 Apr 30 14:19 4654-S118_S22_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5720280947 Apr 30 14:18 4654-S120_S24_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 7411907 Apr 30 14:18 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples_with_both_overhangs.txt -rw-rw---- 1 dz33 dcistat 0 Apr 30 14:18 4654-S131_S35_L001_trash_out -rw-rw---- 1 dz33 dcistat 6040709 Apr 30 14:18 4654-S131_S35_L001_junction_counts_more_than_8_in_all_samples.txt -rw-rw---- 1 dz33 dcistat 10488834 Apr 30 14:18 profiled_4654-S131_S35_L001_Aligned.out.spanning_junction_reads_junction_overhang_mapped_num.txt -rw-rw---- 1 dz33 dcistat 5420332693 Apr 30 14:18 4654-S134_S38_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5491703218 Apr 30 14:18 4654-S115_S19_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5141566167 Apr 30 14:17 4654-S136_S40_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5211590591 Apr 30 14:17 4654-S113_S17_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5185754596 Apr 30 14:17 4654-S114_S18_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5091153865 Apr 30 14:17 4654-S116_S20_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 5028159806 Apr 30 14:16 4654-S117_S21_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4883663549 Apr 30 14:16 4654-S130_S34_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4816860842 Apr 30 14:16 4654-S119_S23_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4492050834 Apr 30 14:15 4654-S133_S37_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4339330913 Apr 30 14:15 4654-S135_S39_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4669802889 Apr 30 14:15 4654-S132_S36_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4635096659 Apr 30 14:14 4654-S129_S33_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4171558121 Apr 30 14:13 4654-S131_S35_L001_Aligned.out.spanning_junction_reads.bed -rw-rw---- 1 dz33 dcistat 4801920589 Apr 30 14:11 4654-S118_S22_L001_Aligned.out.spanning_junction_reads.bam -rw-rw---- 1 dz33 dcistat 4681372927 Apr 30 14:11 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
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.
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.
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Thank you very much! Will try it and let you know.
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.