bamTobw

Convert BAM files to bigWig files with a simple command

Advantage

• Enable to scale expression signals to HPB (Hits Per Billion-mapped-bases). More information about HPB refer to Zhu S*, Xiang JF*, Tian C, Chen LL# and Yang L#. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. BMC Genomics, 2013, 14:206.
• Enable to divide the BAM file according to the strand information of each read

Usage

bamTobw.sh -- convert stranded sequencing BAM file to bigWig file
Usage: bamTobw.sh -b <bamlist> [-s] [-d] [-l <readlength>]
-b <bamlist> -- file contains bam files (one file per line)
-s -- if set, related files will be scaled to HPB
-d -- if set, bam file will be divide into strand plus and strand minus
-l <readlength> -- you could assign it instead of reading from bam file

Note: -d is only suitable for single reads, not for paired-end reads.

Requirements

• samtools
• UCSC utilities
• bedtools

Note

For stranded sequencing, the default sequencing protocl is dUTP methods. More discussions please refer to issue #1.

This tool is suitable for different sequencing types and trimmed reads. See issue #2.

License

Copyright (C) 2014 YangLab. See the LICENSE file for license rights and limitations (MIT).