Dear Gviz guys,

Unfortunately I am getting a weird off-by-one error when trying to plot coverage and reads from a STAR alignet BAM file. This error is only present in Gvit and not in IGV:

https://www.dropbox.com/s/phh49m83iye0kmz/Gvizoffbyone.jpeg?dl=0

https://www.dropbox.com/s/3gpu5l3pviznznx/igv_snapshot.png?dl=0

My command:

####

achrom <- "chr16"
afrom <- 23649261
ato <- 23649301
mutpos <- 23649285
altrack1 <- AlignmentsTrack(bamfile1, isPaired = FALSE,
    col.mates = "darkgrey", fill = "#E41A1C", type = c("pileup"), 
    name = sample, stackHeight = 0.8, min.height = 4, max.height = 8)

bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = achrom, 
    start = afrom, end = ato, filter = list(with_ox_refseq_mrna = TRUE), 
    stacking = "dense")
axisTrack <- GenomeAxisTrack(labelPos = "below")
ht <- HighlightTrack(trackList = list(bmt), start = mutpos, width = 1, 
    chromosome = achrom, fill = "#000000", inBackground = TRUE)

plotTracks(
    list(altrack1,ht,sTrack,axisTrack),
    from = afrom, to = ato, chromosome = achrom, sizes=c(5,1,1,1), 
    fontcolor = fcol)

####

Any ideas?

Thanks for your great support btw!

Best, Bernt

Hi Bernt,

looks like a 0 vs 1 offset issue. I am a bit surprised that this did not occur earlier. Have to check whether something changed in the core tools that we are using for reading the BAM files. Is there a chance that you could upload the section from bamfile1 shown in you example to that drop box location? Would be easiest for me to fix if I had that.

Florian