BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
For detailed information, visit the wiki page
Clone the libBigWig repository from GitHub: https://github.com/dpryan79/libBigWig
BAMscale cov --bed <BED_FILE> --bam <BAM1> --bam <BAM2> --bam <BAM3> ... --bam <BAMn>
Generating scaled coverage tracks
BAMscale scale --bam <BAM_FILE> [--bam <BAM2> .. --bam <BAMn>]
Build docker image
docker build -t bamscale https://raw.githubusercontent.com/pongorlorinc/BAMscale/master/Dockerfile
Peak quantification with Docker
docker run -v `pwd`:/data bamscale BAMscale cov --bed <BED_FILE> --bam <BAM1> --bam <BAM2> --bam <BAM3> ... --bam <BAMn>
Generating scaled coverage tracks with Docker
docker run -v `pwd`:/data bamscale BAMscale scale --bam <BAM_FILE> [--bam <BAM2> .. --bam <BAMn>]
Public Domain notice
National Center for Biotechnology Information.
This software is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.
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