Question: Different junction numbers from sashimi plot of Gviz package and summarizeJunctions() of GenomicAlignments package
0
gravatar for chengwang29
3.5 years ago by
chengwang290 wrote:

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

 

 

gviz genomicalignments • 987 views
ADD COMMENTlink modified 3.5 years ago by Robert Ivanek610 • written 3.5 years ago by chengwang290
Answer: Different junction numbers from sashimi plot of Gviz package and summarizeJuncti
1
gravatar for Robert Ivanek
3.5 years ago by
Robert Ivanek610
Switzerland
Robert Ivanek610 wrote:

Dear Cheng, Thanks for pointing that out I fixed in the release version, the fix in devel should come soon.

The fixed release version is 1.14.1

Best

Robert
 

ADD COMMENTlink written 3.5 years ago by Robert Ivanek610
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