dieterich-lab JACUSA2 issues

dieterich-lab / JACUSA2

New version of JACUSA -> 2.0

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issues

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Question about splitting reads that contain Ns in their cigar string

#80 gianfilippo closed 1 week ago
2
question about overlap between JACUSA2 and REDItools

#79 gianfilippo closed 1 week ago
4
Strandedness Issue -- opposite results for Reditools2 and JACUSA2

#78 ekofman closed 3 weeks ago
4
non standard VCF output ?

#77 gianfilippo closed 3 weeks ago
2
Need suggestion/advice regarding JACUSA pileup

#76 aayushraman opened 3 months ago
2
Library type and difference between call-up & pileup

#75 aayushraman closed 4 months ago
4
java.lang.IllegalArgumentException

#74 ericmalekos closed 4 months ago
2
JACUJA2 Code Example Request

#73 Chan-W00 opened 5 months ago
3
GT field of the VCF output

#72 tszkwanyau opened 7 months ago
1
Again pCalc error

#71 H1889 opened 9 months ago
0
Understanding/filtering RRD jacusa2 output

#70 CelineLabbeCurie opened 9 months ago
1
How to appropriately interpret & utilize strand information in call-1

#69 Sfeng666 opened 10 months ago
1
How do general filterings on MQ, BQ and coverage work together?

#68 Sfeng666 opened 10 months ago
1
Jacusa2 Call 2

#67 HaiderMDev closed 1 year ago
2
What is the best practice to prepare input bam files for calling RNA editing ?

#66 YibiChen opened 1 year ago
0
Problems writing file with multithreading

#65 Izar-de-villasante opened 1 year ago
1
complains about "the output is not to a file" with -r variable specified:

#64 Izar-de-villasante opened 1 year ago
0
Unknown output format: /

#63 CelineLabbeCurie opened 1 year ago
5
Bump htsjdk from 2.12.0 to 3.0.1

#62 dependabot[bot] opened 1 year ago
0
z score threshold

#61 anafilia closed 2 years ago
1
bug in script add_seq.sh

#60 atanzer closed 2 years ago
1
feature request - read start and end rate reporting in pileup

#59 joegeorgeson opened 2 years ago
1
paired-end pileup with annotation file - question

#58 joegeorgeson opened 2 years ago
4
java issue with v2.0.1

#57 joegeorgeson opened 2 years ago
4
RNA-seq and DNA-seq data were mapped to different reference genome

#56 YiweiNiu opened 2 years ago
7
How to consider a site as m6A modified

#55 FDallaPozza closed 2 years ago
7
chi square test for likelihood ratio?

#54 fishercera opened 2 years ago
2
True editing sites

#53 ryrl9703 closed 2 years ago
2
Usage of the parameter -B

#52 5Tony closed 2 years ago
2
Download the latest release with Linux cmd line

#51 AminaLEM opened 2 years ago
0
filtering artifacts using -a E:filename

#50 BreenMS opened 3 years ago
2
java.nio.BufferUnderflowException

#49 YibiChen closed 3 years ago
1
Support zero depth sites

#48 y9c opened 3 years ago
2
Number of modifications halfed in JACUSA 2.0 vs. 1.3 (mode call-2)

#47 ckuenne opened 3 years ago
8
-B A2G output format explanation

#46 ckuenne opened 3 years ago
2
JACUSA_to_TRIBE.pl obsolete?

#45 ckuenne opened 3 years ago
3
Pipeup exception

#44 shuzhouliu opened 3 years ago
0
pipeup exception

#43 shuzhouliu closed 3 years ago
0
Error with bed file and rt-arrest mode

#42 CDieterich closed 2 years ago
3
Bump junit from 4.12 to 4.13.1

#41 dependabot[bot] opened 3 years ago
0
No variants called, but no error message

#40 ellalalalalalala closed 3 years ago
4
-v VCF (copied from JACUSA1 - issues)

#39 piechottam opened 3 years ago
2
The jacusa2 result lost the last base(amplicon data)

#38 elaine-bio opened 3 years ago
1
Error: No enum constant jacusa.io.FileType.--VCF

#37 XRCHAM closed 2 years ago
2
For BaseSubResult error(java.lang.NullPointerException)

#36 XRCHAM closed 2 years ago
5
Pileup output

#35 AminaLEM closed 3 years ago
1
Dead Manual link

#34 CDieterich closed 3 years ago
1
Run with replicates

#33 YibiChen closed 3 years ago
1
Peculiar coverage problem on Nanopore data

#32 CDieterich closed 3 years ago
2
call-2 and -u DirMult:calcPvalue crashed

#31 CDieterich closed 3 years ago
0