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Old 10-16-2015, 02:55 PM   #2
mattanswers
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Location: Boston

Join Date: Oct 2009
Posts: 65
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.
Attached Files
File Type: txt TNFAIP3_biomart.txt (13.6 KB, 1 views)
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