# HG changeset patch
# User romaingred
# Date 1507882817 14400
# Node ID 42bc59c7db3a36faee16f0cad08b6683f93602c6
# Parent  0ee4dadfdca39efcc2e04d4bb364385580c46b43
Uploaded

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
@@ -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