BigWig to Bed file format

[Niamh Ryan]

Hi,
I was wondering if you have any advice on converting BigWig data to Bed
file format?
Specifically, I want to access the data in the file
/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign100mer.bw
and see what the mapability scores are for a list of SNPs I have (SNPs.bed).

I know that Galaxy has a tool that allows this conversion, but my SNP
list is large and I want to be able to do this through the command line.

Any suggestions would be very much appreciated.

Many thanks,
Niamh


Niamh Ryan
PhD student

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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Steve Heitner]

Hello, Niamh.

We have a number of utilities available for download at
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. We have a utility
to convert bigWig -> wig, but not bigWig -> bed or even wig -> bed. The
closest thing we have would be bigWig -> bedGraph. You can review the
bedGraph file format at http://genome.ucsc.edu/FAQ/FAQformat.html#format1.8
to see if perhaps this would suit your needs.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions.

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Steve Heitner
UCSC Genome Bioinformatics Group

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