bigwig2bam utility

bigwig2bam is a small rust program to convert bigwig file to bam file

Installation

You need cargo installed

• curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
• sudo apt install cargo
• sudo pacman -S rust
• brew install rust

Then run the following command:

sh cargo install --git http://gitbio.ens-lyon.fr/LBMC/Bernard/bigwig2bam.git

You can also use the lbmc/bigwig2bam:0.1.1 Docker image

sh docker run -it lbmc/bigwig2bam:0.1.1 bamcalib

Usage

Example

sh bamcalib \ --bigwig IP_11.bigwig \ --fasta genome.fasta \ --bam IP_11.bam \ --read_length 150

The bigwig2bam expect the following parameters:

• --bigwig <bigwig_file> bigwig file to convert
• --fasta <fasta_file> fasta genome from which to generate the read sequences
• --output-bam <bam_file> output bam file (sorted)

Optional Arguments

• -c, --cal-prefix <cal_prefix> calibration prefix added to the chromosome name of the calibration genome (default: calib_)
• --read_length <value> size of the reads to generate
• -h, --help Print help information
• -V, --version Print version information