A bit of background. We used the following protocol:
3C RE is HindIII with the following seq A^AGCTT
4C RE is DpnII with the following seq ^GATC
exptData <- SimpleList(projectPath =projectPath,
fragmentDir = "re_fragments",
referenceGenomeFile = referenceGenomeFile,
reSequence1 = "AAGCTT",
reSequence2 = "GATC",
primerFile = primerFile,
bamFilePath = bamFilePath)
Bait primer was trimmed before aligning the reads to the reference (76bp -> 51bp reads). After mapping only reads with MPQ >20 were selected.
It is unclear to me what command and options I should use when counting overlaps. countFragmentOverlaps? or countFragmentOverlapsSecondCutter? and the bases to trim?
I used different trimming values. WIth default values I get the following scatter plot.
fc <- countFragmentOverlaps(fc)
fc <- combineFragEnds(fc)
fc <- smoothCounts(fc)
plotScatter(fc[,c("chr14pv_A1", "chr14pv_A2")], xlab="Rep1", ylab="Rep2", asp=1)
When trimming 1bp I am getting the following.
Trimming 2bp ..... More than 2bp barely produces any dots.