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Commit message:
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modified:
bin/align.pm |
| b |
| diff -r 0ee4dadfdca3 -r 42bc59c7db3a bin/align.pm --- a/bin/align.pm Fri Oct 13 03:17:10 2017 -0400 +++ b/bin/align.pm Fri Oct 13 04:20:17 2017 -0400 |
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| @@ -310,8 +310,8 @@ $bedgraphM = $1.'_minus.bedgraph'; } `samtools view -Shb --threads $number_of_cpus $sam | samtools sort -O BAM --threads $number_of_cpus /dev/stdin > $bam_sorted`; - `bedtools genomecov -scale $scale -strand + -bg -ibam $bam_sorted > $bedgraphP`; - `bedtools genomecov -scale $scale -strand - -bg -ibam $bam_sorted > $bedgraphM`; + `bedtools genomecov -scale $scale -strand + -bga -ibam $bam_sorted > $bedgraphP`; + `bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`; } sub sam_sorted_bam |