bigWigToBedGraph with BED file input

[Gert Hulselmans]

Hi,

It would be nice if bigWigToBedGraph (and for consistency bigWigToWig)
would support BED as interval input instead of only allowing -chrom,
-start, -end.

Now I need to run bigWigToBedGraph 20000 times to get all regions.

$ bigWigToBedGraph
bigWigToBedGraph - Convert from bigWig to bedGraph format.
usage:
bigWigToBedGraph in.bigWig out.bedGraph
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

$ bigWigToWig
bigWigToWig - Convert bigWig to wig. This will keep more of the same
structure of the
original wig than bigWigToBedGraph does, but still will break up large
stepped sections
into smaller ones.
usage:
bigWigToWig in.bigWig out.wig
options:
-chrom=chr1 - if set restrict output to given chromosome
-start=N - if set, restrict output to only that over start
-end=N - if set, restict output to only that under end
-udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs


Thanks,
Gert

[Cath Tyner]

Hello Gert,

Thank you for using the UCSC Genome Browser and for submitting your feedback regarding bigWigToBedGraph (and bigWigToWig) supporting BED as interval input instead of only allowing -chrom, -start, -end.

We appreciate your feedback and have noted your suggestion. In the meantime, below are resources which may be helpful to you:

1. WiggleTools
http://www.ensembl.info/blog/2013/12/23/wiggletools-a-pocket-calculator-for-very-large-datasets/
https://github.com/Ensembl/WiggleTools

2. bwtools
http://www.ncbi.nlm.nih.gov/pubmed/24489365
https://github.com/CRG-Barcelona/bwtool/wiki

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

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​Enjoy,​

Cath
. . .

Cath Tyner

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Gert Hulselmans]

Thanks for the suggestions.

I knew about bwtools (as I was using it already).
WiggleTools seems interesting too.

- Gert