yanglab/bamtobw

Convert BAM files to bigWig files with a simple command

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).

bamtobw's Issues

Plus and minus strands inverted

Hi there,

Thank you for making a great script available. I have been using it on a recent batch of sequencing data but have noticed that the plus and minus stranded bigwigs are the opposite to what we were expecting.

After checking through the script, it looks as though the F and f flags are the wrong way around at lines 20 and 22 in the bam_divide function, what do you think? I.E for forward strands, samtools command should be 'samtools view -F 20' and for reverse, 'samtools view -f 16'

How to deal with trimmed reads?

Hello Xiao-Ou,
You write a useful tool to convert bam to bw format.
I have two questions:
1. How to deal with trimmed reads (the length of each sequence is not equal)?
2. Is this tool suitable for both SE and PE sequencing data sets?