shrink_bedgraph - reduce resolution/size of bedgraph files
shrink_bedgraph --fa fasta --bg in_bedgraph --out out_bedgraph ...
shrink_bedgraph reduces the resolution of a bedgraph file in order to reduce file size and simplify plotting. This is done by binning depth values and applying a summary function to each bin, utilizing samtools and bedtools under the hood. Adjacent entries with identical depths are also merged. A separate optimum bin width is calculated for each contig in the input.
Path to the input bedgraph file
Path to the input FASTA file corresponding to the input bedgraph
Path to which to write the output bedgraph file
Number of bins into which to divide each contig (default: 500)
Summarization operation to apply to each bin. This is passed through directly to the bedtools map call. (default: 'max')
Show documentation and exit
Print version string and exit
Please report all bugs or suggestions on the software repository issues page.
Jeremy Volkening (jeremy.volkening@base2bio.com)
Copyright 2021-2023 Jeremy Volkening
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.