checking overlap between two genomic coordinates

Question

[kanwarjag]

I have two different Chipseq datasets files with peak coordinates. and other information like gene name etc. I want check the overlap of coordinates in two files. Is there any online tool that can help me in checking the overlap between two files. Thanks

Kanwar

[michael.j.apostolides]

In my opinion the most clean way to do this is using bedtools intersect. This is the most standard and "old school" way, and can be easily integrated into pipelines with only one easy to install dependency (bedtools)

[Ram]

Hi, an answer with bedtools intersect already exists. If you have more to add, please add it as a comment to that answer so people going down that path can find all relevant information in the same thread.

[Tm]

If you have gene annotation in gff/gtf format and reference genome fasta with you, then it is very easy to annotate peaks using annotatePeaks.pl, a perl script which is a part of HOMER package.

Command goes like this:

perl annotatePeaks.pl sample_peak.bed Reference_Genome.fasta -gft Reference_genome_annotation.gft   >homer_annotation.txt

[GenoMax]

Original question is not about annotating peaks. It is for finding overlap between two sets.

Answer 1

[Ram]

findOverlaps from GenomicRanges might be of use. See: https://stackoverflow.com/questions/19101849/overlapping-genomic-ranges

Answer 2

[jordi.planells]

You can also try bedtools intersect. See here for more details

Answer 3

[Shalu Jhanwar]

Have a look at BedSect and Galaxy online platforms.