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get only final "genome" line, not chromosomes having 'genome' in their
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name like in dm6
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steffenheyne committed Sep 6, 2016
1 parent b1850f6 commit db5fedc
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion shared/rules/MACS2.snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,7 @@ rule MACS2_peak_qc:
# compute peak genome coverage
cmd = ("sort -k 1,1 "+params.peaks+" | "+
bedtools_path+"genomeCoverageBed -i - -g "+params.genome_index+" | "+
"grep -P 'genome\t1' | cut -f 5"
"grep -P '^genome\t1' | cut -f 5"
)
genomecov = float(subprocess.check_output( cmd, shell=True).decode())

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