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2.1 years ago by
bernt.popp0 wrote:

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

modified 2.1 years ago by Robert Ivanek590 • written 2.1 years ago by bernt.popp0
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2.1 years ago by
Robert Ivanek590
Switzerland
Robert Ivanek590 wrote:

Hi Bernt,

You can set the parameter sashimiNumbers  to TRUE. Then it should work. Either  when you create the track or when using plotTracks function.

Best

Robert

--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  to TRUE ?

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: function readGAlignments or readGAlignmentPairs to read in the data from BAM file and summarizeJunctions to produce the counts for junctions.

ok thank you so much for this help.