Wig Bed Overlap

Nick

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Join Date: Jun 2009

Posts: 16
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#1

Wig Bed Overlap

03-15-2012, 08:18 AM

Hi All,
I want to trim my wig file to contain only regions that are overlapping features in a bed file. Anyone know a way to do this? Trying not to code up something when it seems like it should be something people want to do.
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Orr Shomroni

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Join Date: Oct 2011

Posts: 26
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#2

10-10-2014, 07:54 AM

Not sure if you solved the problem yet, but I found a possible solution: bigWigAverageOverBed returns a table with the following columns:

name - name field from bed, which should be unique
size - size of bed (sum of exon sizes
covered - # bases within exons covered by bigWig
sum - sum of values over all bases covered
mean0 - average over bases with non-covered bases counting as zeroes
mean - average over just covered bases

You can find the code on this website:

Index of /admin/exe/linux.x86_64

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

"Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature
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