Genome-wide distribution of binding sites

[tec]

Hello!

I'm working in ChIP-Seq analysis of transcription factors using Illumina sequencing. After mapping (ELAND) and peak finding (FindPeaks - Thanks to Anthony!!!) i'm happy to have the coordinates of potential binding sites.

Now i’m interested in placing the peaks into genomic context in the form of intergenic regions, genes, intros, exons, promoters and so one with reference to the human genome (or RefSeq genes..). Can anyone recommend a tool or something to manage this question?

Furthermore is there any recommendation for an automated output of the sequence from the start to the end coordinate of the identified peaks in order to look for consensus motifs inside the peaks?

Best regards!
tec

[kopi-o]

If you are comfortable using command-line tools, you could look into cisGenome, which has the functionality you are looking for. You can use Galaxy or the UCSC Genome Browser (out of many possible tools) for extracting sequences from coordinates.

[tec]

Hello kopi-o,

thanks for your answer! I will check cisGenome..

In order to extract sequences from coordinates please could you explain the procedure a little bit more detailed? I have the output files from FindPeaks and want for each Peak max. coordinate the sequence +/- 200 bp. How can i manage this?

Regards! tec

[Chipper]

Hi,

I have made a few scripts for this, if you want to try it send email/pm. To get sequences, covert peak max to bed format (chr start stop) in excel and upload as custom track at UCSC, then select Tables / custom track / sequence.