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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
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