Generate bed file containing regions with no bigwig coverage

Question

[mmmmcandrew]

Hey all-

I would like to find regions in a bigwig file which do not have a score (excluding regions with a score of 0 or more) and output as a bed file. Does anyone know of an easy way to do this? The bigwig files simply contain no data where there is no score (i.e. there is not a "location: no score") value, so it would have to be compared to the entire genome. I also have to use bigwig as the input, so something like bedrolls genomecov wouldn't work for me, since it takes BAM as input.

Thanks!

[mmmmcandrew]

As a follow up to this, I would like to be able to generate random regions in a bed file which excluded all of the regions where there is no score in the bigwig file. It doesn't seem that bedtools random has a mask option, however. Is there an alternative where I could generate random regions that excluded certain portions of the genome?

Answer 1

[Pierre Lindenbaum]

I would like to find regions in a bigwig file which do not have a score

convert the wig to bedgraph : https://genome.ucsc.edu/goldenpath/help/bigWig.html

use awk to filter out the region having a value lower than your treshold.

also use 'bedtools complement' to find the regions not covered by the bedgraph.

[mmmmcandrew]

Thanks Pierre, this worked very nicely to allow me to find regions where we simply didn't have coverage from our sequencing data.