Wig Bed Overlap

[Nick]

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.

[Orr Shomroni]

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:

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