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bernt.popp • 0
@berntpopp-11398
Last seen 4.9 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

Gviz sashimi sashimi plots read counting bam • 1.2k views
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Robert Ivanek ▴ 710
@robert-ivanek-5892
Last seen 1 day ago
Switzerland

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

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--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 --

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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.

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ok thank you so much for this help.