qqwang-berkeley JUM issues

qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns

MIT License

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issues

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adjusting for covariates

#57 SaraAlidadiani opened 4 days ago
0
JUM_C.sh

#56 SaraAlidadiani opened 2 weeks ago
4
JUM_A error

#55 DianavdH opened 2 weeks ago
0
JUM_A.sh error

#54 jaclynmf opened 2 months ago
0
Error while running JUM_A.sh

#53 Yogita121984 opened 2 months ago
0
Error when running JUM step A

#52 hvicars opened 8 months ago
21
JUM_2-3.sh missing in JUM_3.0.0

#51 larysa-27 closed 1 year ago
0
Error when running JUM_A.sh

#50 RacconC opened 1 year ago
0
JUM_A: ERROR: ... not sorted lexicographically

#49 NeuzaRM opened 1 year ago
1
Regarding Error "NONE" after running JUM_C.sh

#48 heebaanjum closed 1 year ago
1
Regarding delta-PSI value, control-treatment vs treatment-control

#47 varamhcu closed 1 year ago
1
_trash_out file should be empty!

#46 rLannes closed 1 year ago
2
JUM a lot of error... but finish runnnig an output empty file.

#45 rLannes closed 1 year ago
1
Perl Error due to a sample not having AS on one contig

#44 rLannes closed 1 year ago
2
perl errors while running JUM_B

#43 dzijlmans opened 2 years ago
1
filtering outputs from cutoff p-value=1

#42 avantika-insitro opened 2 years ago
3
Error of Rscript at write.table step

#41 farzaneafzali closed 2 years ago
1
JUM (v2.0.2 and up) stops and get killed at a certain step

#40 farzaneafzali closed 2 years ago
6
Correcting for batch effects while running JUM

#39 avantika-insitro opened 2 years ago
1
JUM output Splicing events Visualization tools

#38 shashibioinfo143 closed 3 years ago
1
Recommendations for sequencing depth

#37 krisscrim closed 3 years ago
1
error occurred when running JUM_B.sh

#36 mhjiang97 opened 3 years ago
1
PSI values per condition

#35 lhdo closed 3 years ago
1
Can JUM be run on a single bam file ( only one treatment bam or only one control bam)

#34 itszhengan closed 3 years ago
6
The length of the RNA-seq reads is inconsistent

#33 AY-LIANG closed 4 years ago
0
How to match sub-junctions to PSI value in composite events?

#32 angel-bee2018 closed 4 years ago
2
Huge amount of space required!!!

#31 Yago-91 closed 3 years ago
1
Uninitialized value errors when running JUM_C.sh

#30 lindayqlin opened 4 years ago
8
AS junction co-ordinates are sometimes wrong.

#29 angel-bee2018 opened 4 years ago
3
can --Condition1_fileNum_threshold and --Condition2_fileNum_threshold be unequal?

#28 itszhengan closed 4 years ago
2
Potential missing "

#27 Paterson91 closed 3 years ago
1
Empty results of JUM_C.sh; lots of perl errors again

#26 acesnik closed 5 years ago
3
NA qvalues

#25 snallu opened 5 years ago
0
Run time for JUM_B.sh

#24 adt0023 opened 5 years ago
2
Tons of stderr output; problem with preparing_intron_retention_count_table_short_intron.pl

#23 acesnik closed 5 years ago
6
second pass STAR

#22 lindongdo closed 5 years ago
2
Why the input needs different format of sam and bam?

#21 DadongZ closed 5 years ago
11
regarding input files

#20 MurliNair closed 5 years ago
5
Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

#19 LOYON2019 closed 5 years ago
16
Error running R_script_JUM.R

#18 kjsawicka closed 6 years ago
0
adding covariates

#17 jackhump closed 6 years ago
3
total AS events output just contain intron_retention

#16 huiWyuan closed 6 years ago
5
Adding threads to JUM_2-3.sh job submission

#15 binasu closed 6 years ago
8
Purl programs not found in bin folder

#14 lakeofcoheeries closed 6 years ago
1
CREATE LICENSE

#13 qqwang-berkeley closed 6 years ago
0
Rename determining_rightful_long_intron_retention_event.pl to bin/det…

#12 qqwang-berkeley closed 6 years ago
0
Delete JUM_3.sh

#11 qqwang-berkeley closed 6 years ago
0
Issue with JUM_3.sh script

#10 MDBrokaw closed 6 years ago
20
License + open-sourcing development

#9 olgabot closed 6 years ago
1
Missing the AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt file

#8 jamespblloyd closed 6 years ago
0