Hi,
Gviz is an amazing package. But I found that the junction numbers reported from sashimi plot were quite different from the junction numbers generated by “summarizeJunctions” command from GenomicAlignments package. I got junction numbers with following codes:
# Gviz
library(Gviz)
afrom<-2960000
ato<-3160000
alTrack <- AlignmentsTrack(system.file(package = "Gviz","extdata","gapped.bam"), isPaired =T,chromosome="chr12",genome="hg19")
plotTracks(alTrack, from = afrom, to = ato,chromosome = "chr12",type=c("coverage","sashimi","pileup"))
# GenomicAlignments
library(GenomicAlignments)
tmp<-readGAlignmentPairs(system.file(package = "Gviz","extdata","gapped.bam"))
juncs<-summarizeJunctions(tmp)
The largest junction numbers from GenomicAlignments is 30, but junction numbers in Gviz plot seems to be less than 20. I’m confused with this difference. Please advise. Many thanks.
Plus: I noticed that the junction numbers from GenomicAlignments were basically consistent with those from IGV sashimi plot.
Cheng
