Inverse Of An Annotation Track In Bed Format?

Question

[nisha8989]

Hi there,

I am hoping to get some help with the following problem.

I am trying to compare two tracks- DNaseI track from UCSC (BigWig file and a custom track of CNVs (BED file). Specifically, I want to find the degree of overlap, how well or poorly they overlap with each other. I have read that BEDTools is the way to go and will be using that program.

My problem is that I need the INVERSE of the DNaseI track that I got from UCSC. How do I get the inverse of this track? I am looking at first converting its format from BigWig to BED. I do not know how to convert the file so that I obtain an inverse of the track.

Help is much appreciated.

Thank you!

Nisha

Answer 1

[Pierre Lindenbaum]

what to you mean with INVERSE: the complement ?

use bedtools complement ? http://bedtools.readthedocs.org/en/latest/content/tools/complement.html?highlight=complement

[PoGibas]

+1 This is an easy way to get intron coordinates having exons.

Answer 2

[Alex Reynolds]

UCSC Kent tools includes bigWigToBedGraph, which should help with conversion to a BED-like format.

You can also use the bedops utility in BEDOPS to do fast set complements between sorted BED files.

You could get the chromInfo table information from the UCSC Genome Browser to define chromosome bounds for the organism and build of interest, then follow with bedops --complement -L to do a left-edge-bounded set complement of your tracks. Some more discussion of this general procedure is available here.