Hello everyone, I am a beginner in this field.
Actually, my question is about ChIP-Seq data analysis, I have tried ChIP-Seq data analysis for BRCA1 protein (Human) with two replicates. The data quality is good and I have successfully reached at the step of peak calling.
I have used bowtie for raw read alignment and MACS14 for peak calling. At the end of this I got 96483 peaks.
Is it possible that one successful ChIP-Seq experiment could have these many number of peaks? OR if I want to reduce the number of peaks which criteria is better? I have already tried FDR (%) [reported at http://onetipperday.sterding.com/2013/08/how-to-select-macs-peaks-based-on-p.html]. but by using FDR (%) filter I hardly able to discard 10 peaks. In case of pValue criteria peaks have been already filtered by MACS14.
Any help would be really appreciated.