I have a pair of chipseq. One is really bad. Mapping failed.
I was wondering if it's possible to analyse only one without the pair ?
Other question :
I tried to do the analyze with both of the samples even is one is not very good.
I did two different things : the first time I set the rule that peaks must be in both replicates...that gaves me 1116 differential peaks.
dba_chip_consensus <- dba.peakset(dba_chip, consensus=c(type),minOverlap=0.99)
Then I apply the following rule : the peaks must be at least in one or the other replicate. It gave me 1000 differential peaks.
dba_chip_consensus <- dba.peakset(dba_chip, consensus=c(type),minOverlap=0.01)
Strange, no ? I was hoping that it gaves me more peaks using one or the other... Is that possible ?