[Bioc-sig-seq] analysis ChIP-seq data

Bogdan Tanasa tanasa at gmail.com
Wed Jun 11 06:39:56 CEST 2008

Hi everyone.

I would like to have your comments on the best way to analyze the
ChIP-seq data in order to identify the peaks of TF binding.
We have used Solexa alignment program (ELAND) to align the sequences
and I do have the genome coordinates for all the
tags. The question I want to address now is : what is the best model l
to use in order to select the peaks in the data
(and what is the most appropriate cut-off for the number of tags in a peak) ...

Any suggestions will be greatly appreciated. Thanks very much.


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