I would like to use FindPeaks to call peaks on chIP-seq data, where I have an IP against a sequence specific transcription factor, using Input as control. I would appreciate any guidance as to which control methods, cutoff and FDR methods people are using.
I am currently running MACS and SWEMBL also, and though I get good agreement between these two, I do not get very good agreement with findPeaks.
Specific command line options or general guidance about use would be helpfil. I am using it on pre-filtered (on alignment score) BAM files.