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Old 10-08-2015, 08:29 AM   #1
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Location: TX

Join Date: Oct 2015
Posts: 2
Default Is there a way to annotate individual protein peaks within a gene?

Hello everyone!

I'm relatively new to Bioinformatics so please bare with me. A Ph.D student in my lab has asked me to analyze ChIP-Seq data and determine whether peaks fall into exons, introns, or exon-intron junction categories. The gene she is looking at is TNFAIP3 and the mark she wants me to analyze is Pol II. I am using the hg19 human model.

Unsure how to start I did the following:

1) Download BED files for TNFAIP3 and get individual files for Exons, and Introns.

2) Annotate peaks of BED files using a python script already written using Homer.

This however only gives me the annotation of peaks within the entire gene, but the Ph.D student wants to have the individual protein (KAP1, Pol II, etc) peaks annotated in a specific gene region. Is this possible on UCSC? How would I go about it?
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