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

Uploaded

9:0ee4dadfdca3

		$bam_sorted = $1.'_sorted.bam';
		$bedgraphP= $1.'_plus.bedgraph';
		$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`;
}

sub sam_sorted_bam
{
	my ( $sam, $number_of_cpus ) = @_;

10:42bc59c7db3a

		$bam_sorted = $1.'_sorted.bam';
		$bedgraphP= $1.'_plus.bedgraph';
		$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 + -bga -ibam $bam_sorted > $bedgraphP`;	
	`bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`;
}

sub sam_sorted_bam
{
	my ( $sam, $number_of_cpus ) = @_;