1 unstable release
0.1.1 | Feb 28, 2023 |
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37KB
693 lines
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:
cargo install --git http://gitbio.ens-lyon.fr/LBMC/Bernard/bigwig2bam.git
You can also use the lbmc/bigwig2bam:0.1.1
Docker image
docker run -it lbmc/bigwig2bam:0.1.1 bamcalib
Usage
Example
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
Dependencies
~17–25MB
~446K SLoC