Normalized sashimi plots with Gviz

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benjamin.carter • 0

@benjamincarter-20814

Last seen 5.5 years ago

Hello, I have some RNA-seq data and would like to generate sashimi plots to visualize differential exon usage between samples. I would like these plots to be normalized for library size. I would also like to use R if possible to work with existing pipeline. I see that Gviz can generate sashimi plots, but I am not sure if it can normalize the output for library size. Does anyone have any suggestions for how to use Gviz or other R package to accomplish this? Thanks for the assistance!

-Ben

Gviz Sashimi • 1.4k views

ADD COMMENT • link 5.5 years ago benjamin.carter • 0

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Hi Ben, did you find any solution? I have a related question, I want to visualize Mutations in normalized RNA-Seq data...

ADD REPLY • link 5.3 years ago michael ▴ 20

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Can you be more specific? with detailed example?

ADD REPLY • link 5.3 years ago Robert Ivanek ▴ 750

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Hi,

It is currently not implemented to have normalized sashimi plots. Quick solution might be to read-in only fraction of the data and make the figure with imported data instead.

Best Robert

ADD REPLY • link 5.3 years ago Robert Ivanek ▴ 750

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