I am trying to add the "AlignmentsTrack" as coverage and sashimi plot using one of my bam files. However, I get an empty plot as an output.
I've tried using "DataTrack" instead, playing with the max.height and min.height parameters and reinstalling the package but nothing worked. My code is:
#set genome and chromosome gen <- 'hg38' chr <- 'chr1' afrom=93438921 ato=93565861 b1<- 'mysample.bam' #genome axis track gtrack <- GenomeAxisTrack() #ideogram track itrack <- IdeogramTrack(genome = gen, chromosome = chr) #TxDb object txdb <- makeTxDbFromGFF(file="assembled.gtf", organism="Homo sapiens", format = "gtf") #gene track grtrack <- GeneRegionTrack(txdb, genome = gen, chromosome = chr, fill='black', transcriptAnnotation = "symbol", name = "gene", background.title = "darkblue", exon = ex, stacking = 'squish') alTrack <- AlignmentsTrack(range = b1, name = 'data', type= "coverage", isPaired = TRUE, genome = gen, chromosome = chr) plotTracks(c(itrack, gtrack, alTrack, grtrack), from = afrom , to = afrom, chromosome = chr, type = c("coverage", "sashimi"))
Do you have any idea why this could be happening?