I am trying to test the MMDiff2 package on some of my single-end read ChIP-seq data, but getPeakReadsalways returns me error messages (warnings). I cannot get the full package to work. The messages are:
In getReads(P, chroms[j], bam.file, pairedEnd = pairedEnd) :
reads have different read lengths:
The command I used was
MMD <- getPeakReads(MMD, PeakBoundary = 200, pairedEnd = FALSE, run.parallel = FALSE)
I looked at the getPeakReads code ( https://github.com/Bioconductor-mirror/MMDiff2/blob/master/R/getPeakReads.R ) to try to figure it out why I could not get through. If I understood it correctly, I think that pairedEnds is forced to be on all the time.
Could you please help?