Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (input, p300, H3K4me, H3K27Ac and a TF file)--for the histone modification and TF files, I am able to call peaks nicely with in-range FDR%. With the p300 files, however, I am unable to call peaks without FDR % all being very high. My question is why is this happening and how might I correct for this?
My files were aligned using Bowtie for Illumina, then duplicate reads were removed with a run through the Rmdup tool and these are the parameters that I am using:
MACS (on the Rmdup output files)
Effective genome size 1870000000.0
Tag size 40
Band width 300
Pvalue cutoff for peak detection 1e-05
Select the regions with MFOLD high-confidence enrichment ratio against background to build model 40
Parse xls files into into distinct interval files Yes
Use fixed background lambda as local lambda for every peak region Yes
Build the shifting model
Perform the new peak detection method (futurefdr) Yes
Many thanks for any assistance.