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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.
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README.md

BAMscale

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

Reference

Requirements

samtools

http://www.htslib.org/

libBigWig

Clone the libBigWig repository from GitHub: https://github.com/dpryan79/libBigWig

Usage

Peak quantification

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>]

Docker

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.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.

Please cite NCBI in any work or product based on this material.

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