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Chouaref
Snakemake_ChIP_seq_pipeline
Commits
ff65f167
Unverified
Commit
ff65f167
authored
Oct 20, 2021
by
Jihed Chouaref
Committed by
GitHub
Oct 20, 2021
Browse files
Update pre_processing.smk
corrected error in the alignment paired end
parent
52ffe199
Changes
1
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rules/pre_processing.smk
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ff65f167
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@@ -71,8 +71,8 @@ rule align:
shell("bowtie2 --very-sensitive --threads {threads} -x {params.index} \
-U {input.forward_read} | samtools view -Sb - > {output.bams} 2>{log}")
else:
shell("bowtie2 --very-sen
t
itive --threads {threads} -x {params.index} \
-1 {input.forward_read} -2 {input.reverse_read} samtools view -Sb - > {output.bams} 2>{log}")
shell("bowtie2 --very-sen
s
itive --threads {threads} -x {params.index} \
-1 {input.forward_read} -2 {input.reverse_read}
|
samtools view -Sb - > {output.bams} 2>{log}")
rule sort:
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