I'm analyzing H3K4me3 ChIP-seq and i want to find different bound sites using DiffBind.
I have Control samples (7 replicates) and Treated (5 replicates)
After peak calling and load a samplesheet, i have tried to make consensus peak for each condition.
consensus <- dba.peakset(dbObj, consensus = DBA_CONDITION, minOverlap=0.3)
ID Factor Condition Replicate Caller Intervals
13 Control_k4 K4me3 Control_k4 1-2-3-4-5-6-7 raw 46408
14 Severe_k4 K4me3 Severe_k4 1-2-3-4-5 raw 35976
This allow to discard region enriched just in few samples (1 samples in this case) and take in account only "real enriched regions"....right??
Now the question is...how to count reads in this regions using dba.count???
it's conceptually correct or it's wrong?
i'm expected that the regions investigated are 82384 (or less considering that some overlap)...right?
Thanks in advance