nunofonseca irap issues

nunofonseca / irap

integrated RNA-seq Analysis Pipeline

GNU General Public License v3.0

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issues

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Configuration file for strand specific protocol

#108 lissur opened 2 years ago
0
iRAP pipeline for EMBL-EBI Expression Atlas

#107 lissur opened 4 years ago
1
Downloads to a submodule?

#106 pinin4fjords opened 5 years ago
0
Simplify SC preprocessing

#105 pinin4fjords closed 4 years ago
2
fastq_pre_barcodes.c:34:17: fatal error: bam.h: No such file or directory

#104 jianglinghan opened 5 years ago
0
Fix bafflingly introduced typos, do not enforce integer status

#103 pinin4fjords closed 5 years ago
0
sample name do not match

#102 sb43 opened 5 years ago
0
aux/R/irap_de.R::process.cmdline.args mis-casts --min (opt$min_count) as a string, should be integer

#101 vviyer closed 5 years ago
1
modified gnu file open in irap_core.mk to shell cat

#100 sb43 closed 5 years ago
2
No rule to make target

#99 sb43 closed 5 years ago
1
docker image 1.0.1 not working

#98 sb43 closed 5 years ago
1
Add novel splices to output file lists with HISAT2

#97 pinin4fjords closed 4 years ago
0
docker image for v1.0.1

#96 kathryn-beal closed 5 years ago
2
Don't make matrices at top quant level for non-sc data

#95 pinin4fjords closed 5 years ago
0
Fix typo in irap_single_lib2report

#94 pinin4fjords closed 5 years ago
0
Add explict -x for hisat index prefix

#93 pinin4fjords closed 5 years ago
0
Deal with unpredictable index extensions from HISAT2

#92 pinin4fjords closed 5 years ago
0
Change FEATURECOUNTS to FeatureCounts where appropriate

#91 pinin4fjords closed 5 years ago
0
Restore coordinate-sorted bam output

#90 pinin4fjords closed 5 years ago
0
Proper paired-end behaviour for featureCounts

#89 pinin4fjords closed 5 years ago
0
Fix duplicate exon error for featureCounts

#88 pinin4fjords closed 5 years ago
0
iRAP does not recognise stage0 completion for large genomes with HISAT2

#87 pinin4fjords closed 5 years ago
5
Fix to retain Number of reads

#86 pinin4fjords closed 5 years ago
0
Sort before genomecov

#85 pinin4fjords closed 5 years ago
2
Aggregation issues

#84 pinin4fjords closed 5 years ago
0
Reflect change in config file location

#83 pinin4fjords closed 5 years ago
0
Locate manual download folder at same level as raw data download used…

#82 pinin4fjords closed 5 years ago
0
Remove technical replicate group as a compulsory column

#81 pinin4fjords closed 5 years ago
0
Increase memory for sdrf_control processes

#80 pinin4fjords closed 5 years ago
0
Sc3 column names

#79 pinin4fjords closed 5 years ago
0
Better version use

#78 pinin4fjords closed 4 years ago
0
sh: 1: set: Illegal option -o pipefail error in "irap_gtf_to_fasta".

#77 shrho closed 5 years ago
4
Deal with the case of a single single-cell SDRF

#76 pinin4fjords closed 6 years ago
0
Prevent irap_sdrf2conf from dropping metadata dimensions

#75 pinin4fjords closed 6 years ago
0
Fix sc3

#74 pinin4fjords closed 5 years ago
0
Add spike consideration and tidy

#73 pinin4fjords closed 5 years ago
0
Allow for NAs as empty values in technical replicate column

#72 pinin4fjords closed 6 years ago
0
Allow 3D t-SNE plot

#71 pinin4fjords closed 6 years ago
2
Recognise no spikes

#70 pinin4fjords closed 5 years ago
0
Fix bug in fasta from gtf with spikes

#69 pinin4fjords closed 5 years ago
0
Kallisto: handle fragment length better

#68 pinin4fjords closed 5 years ago
1
iRAP's Kallisto call seems to provide read length at fragment size parameter

#67 pinin4fjords closed 5 years ago
1
Allow a Kallisto-specific threads parameter (deterministic output)

#66 pinin4fjords closed 5 years ago
0
Added fix for case where no mappings exist to contamination indices

#65 pinin4fjords closed 6 years ago
0
Parameterise perplexity and increase maximum

#64 pinin4fjords closed 6 years ago
0
Simplify paths

#63 pinin4fjords closed 5 years ago
0
Fix issue due to sudo'd users not having write permission to /dev/stderr

#62 pinin4fjords closed 5 years ago
2
Move scater and SC3 downgrade to end so they don't get re-upgraded

#61 pinin4fjords closed 6 years ago
0
Error running Docker image

#60 larsgtoicr closed 5 years ago
2
Docker link in wiki is wrong

#59 larsgtoicr closed 6 years ago
1