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Old 07-02-2012, 04:57 PM   #1
Kaveh
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Location: USA

Join Date: Oct 2010
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Default Mapping ChIP-Seq data which is in a excel sheet

Hi,

From the supplementary data of a paper, I have an excel sheet that contains the ChIP-seq data. The excel sheet has chromosome number, start and end coordinates of the read and number of reads in the ChIP and background and something like a score (I think it's the peak hight). These are only the selected genes which show binding of the protein.

Now, I want to somehow map this to the genome or have a way to identify those genes. Is there anyway that I can convert those coordinates to gene names? since those read should mainly happen upstream of the gene, would I be able to know the genes next to them?

thanks and I'm sorry about my very poor sequencing knowledge.

-k
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Old 07-03-2012, 12:32 AM   #2
dariober
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So, if I understand this correctly you have a file of binding site positions (peaks) and you want to know which gene is associated to each peak, right? (I doubt the Excel file has *read* positions as it would be a spreadsheet with millions of rows...)

If you have a bed file of gene positions, say "refGene.bed" from UCSC, and you make a bed file of the peak positions, one way to go about your question is to use closestBed from bedtools. This would assign to each peak the closest gene (not tested!):

Code:
closestBed -a peaks.bed -b refGene.bed -D  "b"
This is just one way to address the question. Alternatively, you could use only transcription start site instead of full gene positions if you are interested in binding sites near promoters, and/or windowBed (bedtools again) if you want *all* the genes within a certain distance from each peak.

I would be curious myself to know how other people anwser this problem.

All the best

Dario
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