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Question: Gviz sashimi read count
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gravatar for bernt.popp
8 months ago by
bernt.popp0
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

ADD COMMENTlink modified 8 months ago by Robert Ivanek350 • written 8 months ago by bernt.popp0
1
gravatar for Robert Ivanek
8 months ago by
Robert Ivanek350
Switzerland
Robert Ivanek350 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

 

ADD COMMENTlink written 8 months ago by Robert Ivanek350

--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 REPLYlink written 7 months ago by lmanchon0

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.

ADD REPLYlink written 7 months ago by Robert Ivanek350

ok thank you so much for this help.

 

ADD REPLYlink written 7 months ago by lmanchon0
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