Automation of Sashimi Plot visualization in IGV

[Nathan Salomonis]

Greetings,

I have started using the Sashimi plot viewer in IGV and wanted to see if I could automate visualization of IGV Sashimi plots from the command-line (stand-alone IGV) or through the webstart version of IGV. Basically, I have 100 genome coordinates for splicing events which I would like to automatically export png and svg images for given a known genomic interval of interest.  Is this currently possible?

Thanks,
Nathan

[Jim Robinson]

Hi,

Not its not.  For that I suggest you use the command-line Sashimi plot tool.

Jim

[Nathan Salomonis]

Thanks Jim. We will give that a look.
Best,
Nathan

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[yun YAN]

Hi Jim, 

Do you know whether it is possible to run Sashimi plot without using MISO output? Basically what I need is to plot sashimi plot starting from alignments and gff, just like how the IGV does. 

Best, 

Yun 

[James Robinson]

Hi Yun,  that would be a question for the MISO folks.

Jim

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[yun YAN]

I see. But just for record, I run the sashimi_plot without feeding miso output and it does provide the plot but without the miso estimation. So it works.