Annotating Peaks To Ensemble Build

Question

[ChIP]

Hi!

I have a list of peaks and I would like to annotate them to the nearest genes using ensemble build say 69 or 70.

The desired output is to have the nearest gene and also to know if the peak falls in exon, intron, intergenic or promoter region.

How can I do it?

Kindly help

Thank you

Answer 1

[Sukhi Singh]

Different tools, check out Galaxy Web Interface, If you wanna do offline, try CEAS.

What I do is pull the tables from UCSC(see posts like A: How to download all the introns from UCSC, Format RefSeq output obtained from UCSC Table Browser?) and then use intersectBed from Bedtools. check the usage here A: how to determine overlaps from coordinates. There are lot of posts discussing about this, please skim through archive quickly.

Answer 2

[Steve Lianoglou]

If you are R/Bioconductor inclined, the locateVariants function in the VariantAnnotation package does something similar to what you are trying to do.

Answer 3

[Jordan]

I suggest using, ChIPpeakAnno a package in Bioconductor, R. Here is a link to the paper which talks about the package. It gives you a visual analysis of all the regions near to the peak as well.

Answer 4

[ChIP]

PeakAnalyser from EBI