Hi,

I'd like to show bam reads with mismatches. I use the following code:

plottracks <- function(bpath,spath,chr,from,to) {
    options(ucscChromosomeNames=FALSE)
    seqs <- readDNAStringSet(spath)
    seqTrack <- SequenceTrack(seqs, from=from, to=to, chrom = chr)
    bamTrack<-AlignmentsTrack(bpath, fill.reads="pink", from=from, to=to, chrom = chr)
    plotTracks(c(bamTrack,seqTrack), from=from, to=to, chrom = chr) 
}

plottracks("lg17.bam","lg17.fa","LG17",1693000,1693120)

The resulting plot is here:

How could I prevent reads from overlapping each other? Should I prepare the bam file somehow or is there something wrong in my R code?

Thanks for any help!

Regards, Ari

This is a cross-post, there is also an issue on the Github.

The reason for overlap are too short fragments (shorter than 2*readLength). In case of paired-end sequencing, the mates are always plotted on the same y-coordinate.

You can plot it as a single end data, with this modification:

...
bamTrack <- AlignmentsTrack(bpath, from=from, to=to, chrom = chr, isPaired=FALSE)
...