Tool:Command-Line Software For Bigwig Data

Question

[andypohl]

I made a program that is potentially useful for those working with bigWig data: https://github.com/andypohl/bwtool/wiki

[brentp]

nice documentation, easy to install and nice command-line interface. cheers!

[andypohl]

Hi brentp, thank you. I've never shared any software before, so I'm a little worried about it. I keep trying to add to the web page to limit confusion. I will later add examples of using output from the program in R for plots, or other things like painting chromosomes with UCSC genome graphs.

[dli]

Thanks for sharing this nice tool, Andy!

[homes7]

Hi Andy,

Thanks for your tool! Is it possible to use it to convert a bigWig to a Wig? I have been having an issue with the bigWigToWig tool from UCSC.

Answer 1

[Shicheng Guo]

Share some bigwig commands at the same time:

http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

bedGraphToBigWig
bigWigAverageOverBed
bigWigCat
bigWigCluster
bigWigCorrelate
bigWigInfo
bigWigMerge
bigWigSummary
bigWigToBedGraph
bigWigToWig
wigToBigWig

[ATpoint]

Adding this repository (cgpBigWig) from a group at the Wellcome Sanger Trust, including bg2bw, which reads a bedGraph from STDIN, outputting bigwig (which bedGraphToBigWig still cannot do).

[Shicheng Guo]

Great. Thanks ATpoint.

bwcat   Read the contents of a bigwig (.bw) file
bwjoin  Concatenate bigwig files together
bam2bw  Generate bigwig (.bw) coverage file from bam
bg2bw   Generate bigwig (.bw) coverage file from bedgraph (.bed) format
bam2bwbases Generate bigwig (.bw) proportion file of each base at a position from bam
bam2bedgraph    Generate a coverage bedgraph from bam