I am trying to run the following command:
qseaSet=addCoverage(qseaSet, uniquePos=TRUE, paired=TRUE)
but I keep on getting the error below.
I am running version sea_1.6.0 and running on a custom BSGenome reference. Any suggestions are greatly appreciated.
Reading bam alignment combined_bams/S4_Apo1_ALL_sorted.bam Number of imported sequencing fragments: 13908900 Calculating short read coverage for genome wide windows. Error in data.frame(seqnames = ReadsL[[idx]]$rname[keep], start = pos[keep] + : arguments imply differing number of rows: 0, 1 In addition: Warning messages: 1: In min(isize) : no non-missing arguments to min; returning Inf 2: In max(isize) : no non-missing arguments to max; returning -Inf