Question: checking overlap between two genomic coordinates
0
gravatar for kanwarjag
3 months ago by
kanwarjag1.1k
United States
kanwarjag1.1k wrote:

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

chip-seq • 317 views
ADD COMMENTlink modified 3 months ago by toralmanvar900 • written 3 months ago by kanwarjag1.1k

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)

ADD REPLYlink written 3 months ago by michael.j.apostolides10

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.

ADD REPLYlink written 3 months ago by _r_am31k

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
ADD REPLYlink written 3 months ago by toralmanvar900

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

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax92k
1
gravatar for _r_am
3 months ago by
_r_am31k
Baylor College of Medicine, Houston, TX
_r_am31k wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by _r_am31k
1
gravatar for jordi.planells
3 months ago by
jordi.planells270 wrote:

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

ADD COMMENTlink written 3 months ago by jordi.planells270
0
gravatar for Shalu Jhanwar
3 months ago by
Shalu Jhanwar470
Switzerland
Shalu Jhanwar470 wrote:

Have a look at BedSect and Galaxy online platforms.

ADD COMMENTlink written 3 months ago by Shalu Jhanwar470
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