Mercurial > repos > romaingred > pirna_pipeline

comparison bin/align.pm @ 10:42bc59c7db3a draft

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author romaingred
date Fri, 13 Oct 2017 04:20:17 -0400
parents 198009598544
children 39b039d82743
comparison
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9:0ee4dadfdca3 10:42bc59c7db3a
308 $bam_sorted = $1.'_sorted.bam'; 308 $bam_sorted = $1.'_sorted.bam';
309 $bedgraphP= $1.'_plus.bedgraph'; 309 $bedgraphP= $1.'_plus.bedgraph';
310 $bedgraphM = $1.'_minus.bedgraph'; 310 $bedgraphM = $1.'_minus.bedgraph';
311 } 311 }
312 `samtools view -Shb --threads $number_of_cpus $sam | samtools sort -O BAM --threads $number_of_cpus /dev/stdin > $bam_sorted`; 312 `samtools view -Shb --threads $number_of_cpus $sam | samtools sort -O BAM --threads $number_of_cpus /dev/stdin > $bam_sorted`;
313 `bedtools genomecov -scale $scale -strand + -bg -ibam $bam_sorted > $bedgraphP`; 313 `bedtools genomecov -scale $scale -strand + -bga -ibam $bam_sorted > $bedgraphP`;
314 `bedtools genomecov -scale $scale -strand - -bg -ibam $bam_sorted > $bedgraphM`; 314 `bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`;
315 } 315 }
316 316
317 sub sam_sorted_bam 317 sub sam_sorted_bam
318 { 318 {
319 my ( $sam, $number_of_cpus ) = @_; 319 my ( $sam, $number_of_cpus ) = @_;