MonashBioinformaticsPlatform RNAsik-pipe issues

MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline

https://monashbioinformaticsplatform.github.io/RNAsik-pipe/

Apache License 2.0

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issues

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featureCounts is often slower than it should be

#58 pansapiens closed 9 months ago
1
Pair detection fails for files containing multiple _1 or _R1 substrings

#57 pansapiens opened 3 years ago
1
Output a citation list of tools used

#56 pansapiens opened 4 years ago
2
STAR and index versions

#55 serine opened 4 years ago
0
featureCounts setting paired flag when it shouldn't

#54 serine opened 4 years ago
0
Pair detection fails when pairId appears twice in filename

#53 pansapiens opened 5 years ago
2
picard CreateSequenceDictionary should include -Xmx memory setting

#52 pansapiens opened 5 years ago
0
STAR index generation or mapping with --sjfbGTFfile

#51 pansapiens opened 5 years ago
2
qualimap task should specify memory requirements

#50 pansapiens opened 5 years ago
0
How to include gene descriptions ?

#49 tseemann opened 5 years ago
0
Fatal error: /mnt/software/apps/RNAsik-pipe-1.5.3/bin/../src/sikProcBam.bds, line 21, pos 40. java.lang.Long cannot be cast to java.lang.Double

#48 SpeculativeCynic closed 5 years ago
2
get_geneids.py should fallback to existing IDs if 'nice' ID discovery fails

#47 pansapiens opened 5 years ago
0
Long input filenames break the pipeline

#46 pansapiens opened 5 years ago
1
Ability to explicitly specify pairs

#45 pansapiens opened 5 years ago
0
default fastqc version in conda rnasik needs update

#44 alexyfyf opened 5 years ago
0
Determine if qualimap results are misleading, if so remove/replace it

#43 pansapiens opened 5 years ago
0
Generate *-withNames-proteinCoding.txt counts for each different strandedness option

#42 pansapiens closed 5 years ago
1
include -Q flag to filtering multi-mapping reads from featureCounts

#41 serine closed 5 years ago
1
Allocate samtools memory per-thread.

#40 pansapiens closed 5 years ago
1
Memory set for samtools sort is incorrect, doesn't account for number of threads

#39 pansapiens closed 5 years ago
6
Use any of gene, exon, transcript, CDS in get_geneids.py

#38 pansapiens closed 5 years ago
1
Feature addition request

#37 methylnick opened 6 years ago
3
Pass JVM memory settings to Picard

#36 pansapiens opened 6 years ago
1
Better estimation of strand bias / strandedness

#35 pansapiens closed 5 years ago
7
Fix "java.lang.Long cannot be cast to java.lang.Double" bug

#34 stu2 opened 6 years ago
0
Sample data download in docs

#33 pansapiens opened 6 years ago
0
Prototype sabre - demultiplexing addition to RNAsik

#32 serine opened 6 years ago
0
add into the help the "missing" param --feat_type

#31 methylnick closed 5 years ago
1
get_geneids.py fails to produce output

#30 pansapiens closed 5 years ago
5
fix gtf

#29 alexyfyf closed 4 years ago
0
declaring the reference file directory with -refFiles throws an error

#28 methylnick opened 6 years ago
2
Looking for a BASH master to polish up quick install script !

#27 serine opened 6 years ago
0
issue with mkLog function

#26 serine opened 6 years ago
0
Optionally specify bds.config using environment variable

#25 pansapiens closed 6 years ago
2
error in the pipeline 1.5.0, duplicated gene names in geneID file, and naming error for fastqc report generation

#24 methylnick closed 6 years ago
4
starWithAnn in 1.4.9

#23 alexyfyf opened 6 years ago
6
Cannot install and following the instructions

#22 andrewyatz closed 6 years ago
2
Make Python2/3 compatible (mostly with futurize).

#21 pansapiens closed 6 years ago
0
Issue use -align starWithAnn

#20 alexyfyf closed 6 years ago
0
Accomodating fastq file names from other sequencers (BGISEQ)

#19 methylnick closed 6 years ago
2
FASTQ renaming through samples sheets is broken

#18 serine closed 6 years ago
1
Make Python scripts compatible with Python 3.x and 2.7

#17 pansapiens closed 6 years ago
1
Cannot install bds for RNAsik-pipe

#16 andrewyatz closed 6 years ago
6
Installation Instructions Unclear

#15 andrewyatz closed 6 years ago
1
Help improve `alignerReads` function

#14 serine opened 6 years ago
0
Only check for existence of executables if the run requires it

#13 pansapiens opened 6 years ago
5
fixed typos and formatting of markdown documents so readable in nano

#12 methylnick closed 5 years ago
2
Single end mode - with error exit code 1, not annotating count table with GTF or completing multiqc

#11 methylnick closed 6 years ago
1
Backward compatible

#10 stu2 closed 6 years ago
1
Idx folders not named properly

#9 stu2 opened 6 years ago
1