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Old 10-08-2015, 08:29 AM   #1
Cguzman
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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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Old 10-16-2015, 02:55 PM   #2
mattanswers
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Default mapped reads distributed over genome features

I am not quite sure as to what you mean when you say 'the mark she wants me to analyze'.

Was the ChIP-Seq experiment done with antibodies to KAP-1 or Pol II ?

If this is the case, then PeakRanger (http://ranger.sourceforge.net/ ) is something I have used that will provide a base position for the peak 'summit' if the peaks are not diffuse such as you can typically get with methylation peaks.

Knowing the chromosome and position on that chromosome for TNFAIP3, I think you could use samtools with your alignment .bam or .sam file to get all reads from that region of the genome. Make a file of these reads and format it into BED format.

Then you need a file specifying the start and stop locations of all the exons and introns. Using biomart Tools (http://central.biomart.org/martwizar...8WTSI,%20UK%29) I have made attached a .txt file that may help. A GTF file for hg19 would also help.

You can open this file up in Excel, edit it the way you want, and then format it into into BED format.

Then use BEDtools (http://bedtools.readthedocs.org/en/latest/) on the two BED formatted files to, I think, get what you want.
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File Type: txt TNFAIP3_biomart.txt (13.6 KB, 1 views)
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