Commit 38e6d44f authored by Audrey BIHOUEE's avatar Audrey BIHOUEE
Browse files

ajout cible fpkm. Manque bed

parent 8f04370f
......@@ -120,6 +120,7 @@ rule all:
index=expand(OUTPUTDIR+"/Samples/{sampleName}/STAR/{sampleName}Aligned.sortedByCoord.out.bam.bai",sampleName=SAMPLESALL),
#htseq=expand(OUTPUTDIR+"/DESEQ2/counts/{sampleName}",sampleName=SAMPLESALL)
deg=expand(OUTPUTDIR+"/DESEQ2/results/{suffixe}",suffixe=["NormalizedCountMatrix.txt","NormalizedCountMatrixFiltered.txt","PCAplot.png","sampletosampledistance.jpeg"]),
fpkm=expand(OUTPUTDIR+"/Samples/{sampleName}/STAR/{sampleName}.FPKM.xls",sampleName=SAMPLESALL),
rep=OUTPUTDIR+"/Report/report.html"
rule fastqc:
......@@ -253,6 +254,12 @@ rule htseq:
fi
"""
rule fpkm:
input: OUTPUTDIR+"/Samples/{sampleName}/STAR/{sampleName}Aligned.sortedByCoord.out.bam"
output: OUTPUTDIR+"/Samples/{sampleName}/STAR/{sampleName}.FPKM.xls"
shell: "FPKM_count.py -i {input} -o {wildcards.sampleName} -r {BED}"
rule deseq2_conditions:
output: tab = OUTPUTDIR+"/DESEQ2/DESEQ2_CONDITIONS.tab"
run:
......@@ -270,7 +277,7 @@ rule deseq2:
params: outdir = OUTPUTDIR+"/DESEQ2/results",
countsdir = OUTPUTDIR+"/DESEQ2/counts"
shell: """
cat {SCRIPTPATH}/run_deseq2.R | R --slave --args {input.conditions} {params.countsdir} {params.outdir} {BIOMART}
cat {SCRIPTPATH}/run_deseq2.R | R --slave --args {input.conditions} {params.countsdir} {params.outdir} {BIOMART}
"""
rule deg:
......@@ -281,7 +288,7 @@ rule deg:
shell: """
cat {SCRIPTPATH}/deg.R | R --slave --args {input.rdata} {params.cond1} {params.cond2}
"""
rule annot:
input: expand(OUTPUTDIR+"/DESEQ2/results/{{comp}}/{{comp}}_{file}", file=["All_DEG.tsv","DEseqRes.tsv"]),
corrAnnotations=(SCRIPTPATH+"/corresIDorg.txt"),
......
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