Overlap chipseq regions with repetative regions

Question

[chipseq33]

Hi guys,

I have a list of ChIP regions and I would like to know

1) which of them overlap with RepeatMask table that I took through UCSC?

chr1 10000 10468 + Simple_repeat chr1 10468 11447 - Satellite chr1 11503 11675 - LINE chr1 11677 11780 - DNA chr1 15264 15355 - SINE chr1 16712 16749 + Simple_repeat

2) how much overlap do you consider to say that one given region is located in repetitive regions?

Thanks in advance chip

Answer 1

[James Ashmore]

You can use the command-line tool bedtools for this analysis. Use the intersect command to look for overlaps between your ChIP regions and the regions in the RepeatMask table. You can also specify a minimum overlap required for the region to count as an overlap, in the example below I've set the minimum overlap to be 50% of a ChIP regions length:

bedtools intersect -a ChIP_regions.bed -b RepeatMask_table.bed -f 0.5

Answer 2

[jotan]

If you are interested in identifying ChIP-seq enrichment at repeats, you should take a look at this paper from the Kharchenko lab:

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-6-r69

Source code is available here:

http://compbio.med.harvard.edu/repeats/

This will give a more accurate idea of repeat enrichment compared to mapping reads across the genome.