Mercurial > repos > romaingred > pirna_pipeline

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

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Uploaded
author romaingred
date Fri, 13 Oct 2017 04:20:17 -0400
parents 198009598544
children 39b039d82743
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line diff
--- a/bin/align.pm	Fri Oct 13 03:17:10 2017 -0400
+++ b/bin/align.pm	Fri Oct 13 04:20:17 2017 -0400
@@ -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