Question

Gviz sashimi read count

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bernt.popp • 0

@berntpopp-11398

Last seen 7.8 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 • 2.3k views

ADD COMMENT • link updated 7.8 years ago by Robert Ivanek ▴ 750 • written 7.8 years ago by bernt.popp • 0

score 1 · Answer 1 · 2017-03-08

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Robert Ivanek ▴ 750

@robert-ivanek-5892

Last seen 13 months 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

ADD COMMENT • link 7.8 years ago Robert Ivanek ▴ 750

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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 --

ADD REPLY • link 7.7 years ago lmanchon • 0

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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.