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.

In the wiki page we have more detailed tutorials for:

1. OK-seq and RFD Track Generation
2. Quantifying Peaks
3. Generating Scaled Coverage Tracks
4. END-seq data
5. Log2 Coverage Tracks for Replication Timing Data
6. Smoothening Function for Coverage Tracks

For additional information, visit the wiki page.

BAMscale can be found at bioRχiv (https://doi.org/10.1101/669275)

We have a detailed installation for Linux and MAC (with homebrew) based systems or through conda. There is also a precompiled version for linux ready for usage available at the releases.

http://www.htslib.org/

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

git clone https://github.com/dpryan79/libBigWig.git

Compile it and set the environment variables for BAMscale

cd libBigWig/
make
export LIBBIGWIG_DIR=`pwd`
export CPPFLAGS="-I $LIBBIGWIG_DIR"
export LDFLAGS="-L $LIBBIGWIG_DIR -Wl,-rpath,$LIBBIGWIG_DIR"

Optionally (and if you have permission), the libbigwig can also be installed

make install

In this case, the flags don't have to be set in the terminal.

After compiling the libBigWig library and samtools (if not already installed) clone the BAMscale from GitHub

git clone https://github.com/ncbi/BAMscale.git

and go to the BAMscale folder to compile the program:

cd BAMscale/
make

A bin folder will be created with the BAMscale executable.

BAMscale cov --bed <BED_FILE> --bam <BAM1> --bam <BAM2> --bam <BAM3> ... --bam <BAMn>

BAMscale scale --bam <BAM_FILE> [--bam <BAM2> .. --bam <BAMn>]

docker build -t bamscale https://raw.githubusercontent.com/pongorlorinc/BAMscale/master/Dockerfile

docker run -v `pwd`:/data bamscale BAMscale cov --bed <BED_FILE> --bam <BAM1> --bam <BAM2> --bam <BAM3> ... --bam <BAMn>

docker run -v `pwd`:/data bamscale BAMscale scale --bam <BAM_FILE> [--bam <BAM2> .. --bam <BAMn>]

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.