Commit 1f9bfa30 authored by Pierre LINDENBAUM's avatar Pierre LINDENBAUM 💬
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Ajout de outSAMattrRGline cf :...

Ajout de outSAMattrRGline cf : http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf 

> string(s):  SAM/BAM read group line.  The first word contains the read groupidentifier and must start with ”ID:”, e.g.  –outSAMattrRGline ID:xxx CN:yy”DS:z z z”.xxx will be added as RG tag to each output alignment.  Any spaces in the tagvalues have to be double quoted
parent 777daa46
......@@ -216,7 +216,7 @@ rule star_PE:
params: cpu=config["align-cpu"]
conda: "CONDA/rnaSeqQuantif.yml"
shell: """
STAR --runThreadN {params.cpu} --genomeDir {GENOMEDIR} --readFilesCommand zcat --outFileNamePrefix {OUTPUTDIR}/Samples/{wildcards.sampleName}/STAR/{wildcards.sampleName} --readFilesIn {input.R1} {input.R2} --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 6
STAR --runThreadN {params.cpu} --genomeDir {GENOMEDIR} --readFilesCommand zcat --outFileNamePrefix {OUTPUTDIR}/Samples/{wildcards.sampleName}/STAR/{wildcards.sampleName} --readFilesIn {input.R1} {input.R2} --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 6 --outSAMattrRGline ID:{wildcards.sampleName} SM:{wildcards.sampleName} LB:{wildcards.sampleName} CN:PFBirdNantes
"""
......
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