Sometimes my ChIP-seq samples do not get any significant peaks by MACS, so the output peaks file is empty. When I use that file in DiffBind sample sheet, I get an error:
Error in read.table(fn, blank.lines.skip = T, header = T) : no lines available in input Calls: dba ... pv.peakset -> pv.readPeaks -> pv.macs -> read.table
Is there a way to suppress that error?
I understand if all the samples have no peaks, there should definitely be an error, but sometimes you have one sample that just doesn't have strong peaks that you still want to include in the analysis.