Entering edit mode
bernt.popp
•
0
@berntpopp-11398
Last seen 7.7 years ago
Hey,
I would like to plot the count of spliced reads supporting the junction above the splice bezier-curve, similar to the original sashimi plot now integrated in IGV.
Is there an option in Gviz for this?
Best, Bernt
--Hi,
is it possible to store in a file the count of spliced reads displayed by the sashimi plot when i set the parameter
sashimiNumbers
toTRUE ?
best,
laurent --
To get those numbers via Gviz seems to me too complicated. You can use package
GenomicAlignments
to get those numbers from BAM files directly: functionreadGAlignments
orreadGAlignmentPairs
to read in the data from BAM file andsummarizeJunctions
to produce the counts for junctions.ok thank you so much for this help.