Question: Normalized sashimi plots with Gviz
0
gravatar for benjamin.carter
4 months ago by
benjamin.carter0 wrote:

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 • 105 views
ADD COMMENTlink written 4 months ago by benjamin.carter0

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

ADD REPLYlink written 5 weeks ago by michael20

Can you be more specific? with detailed example?

ADD REPLYlink written 5 weeks ago by Robert Ivanek640

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 REPLYlink written 5 weeks ago by Robert Ivanek640
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 297 users visited in the last hour