Question: Annotating Peaks To Ensemble Build
0
gravatar for ChIP
7.5 years ago by
ChIP570
Netherlands
ChIP570 wrote:

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

perl python chip-seq • 2.5k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by ChIP570
1
gravatar for Sukhdeep Singh
7.5 years ago by
Netherlands
Sukhdeep Singh10k wrote:

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.

ADD COMMENTlink modified 7 months ago by RamRS28k • written 7.5 years ago by Sukhdeep Singh10k
0
gravatar for Steve Lianoglou
7.5 years ago by
Steve Lianoglou5.0k
US
Steve Lianoglou5.0k wrote:

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

ADD COMMENTlink written 7.5 years ago by Steve Lianoglou5.0k
0
gravatar for Jordan
7.5 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Jordan1.1k
0
gravatar for ChIP
7.5 years ago by
ChIP570
Netherlands
ChIP570 wrote:

PeakAnalyser from EBI

ADD COMMENTlink written 7.5 years ago by ChIP570
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