NAME

bam_split.pl - Split a BAM file by strands

SYNOPSIS

bam_split.pl [--bam FILE] [options]

DESCRIPTION

Split a BAM file by strands and create two new BAM file: One containing all reads that map to the positive strand and another one with all reads mapped to the negative strand. Optionally filter unique alignments by inspecting NH:i SAM attribute.

Optionally create bedGraph and (stranded |normalized) bigWig coverage for UCSC visualization

OPTIONS

--bam

Input file in BAM format

--bed

Create a BED6 file for each split BAM file

--bw

Create BedGraph and bigWig coverage files for e.g. genome browser visualization.

--bwdir

Directory name for resulting bigWig files. This directory is created as subdirectory of the output directory. Default is 'vis'.

--cs

Chromosome sizes file (required if --bw is given).

--norm

Normalize resulting bigWig files

--out -o

Output directory

--reverse -r

Reverse the +/- strand mapping. This is required to achieve proper strand assignments for certain RNA-seq library preparation protocol.

--scale

If --bw is given, scale bigWig files to this number. Default is 1000000.

--uniq

Filter uniquely mapped reads by inspecting the NH:i: SAM attribute. See also the bam_uniq.pl utility, which extracts both uniquely and multiply mapped reads from BAM files without strand-splitting.

--log -l

Log file extension. Default is ".bam_split.log". The log file is created in the directory given via -o and its name is constructed from the base name of the input BAM file and the log filename extension.

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>