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Old 02-27-2015, 04:57 AM   #1
Location: sweden

Join Date: Apr 2013
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Question Consistent peaks from Histone Chip datasets

I have 3 histone-marks Chip-Seq data (H3K27AC,H3K4me3,H3K27me3). Each condition has two biological replicates and 2 controls. I used SICER to call the peaks, and results looks promising .

If there are two biological replicates, how to obtain the consistent islands (signals present in two replicates) . For TF chip , I tried IDR approach to obtain the peaks that are consistent in replicate data.

IDR approach described in above link is for TF chip, can I use the same approach for Histone Chip data?? or is there any other approach that people usually follows, when analyzing Histone Chip with replicate data?

Any suggestions??

Last edited by priya; 03-02-2015 at 01:15 AM.
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