[miso-users] visualizing on genome browser

[Yarden Katz]

Hi Maayan,

There's no tool that does this conversion automatically, but depending on what parts of the output from the summary file you want, it seems straightforward to convert it to a BED file -- which can then be loaded to UCSC.  Some of our users in the past have written code to make UCSC tracks where each exon is plotted as a block with a shading proportional to the Psi value.  You can try doing something like that.

If you have specific ideas on what you'd like as the output, let me know and we can consider making generic features for it in MISO.  I'm not sure what the best and most general conversion of the information MISO outputs into a UCSC-friendly format, but I'm also not a heavy UCSC browser user, so if you have thoughts let me know.

Best, --Yarden

On May 1, 2013, at 4:15 PM, Maayan Kreitzman wrote:

> Hi Yarden,
> I know that Sashimi-plot is built into MISO, I've tried it and it's 
> great. But, we're comparing the poly-A calls miso produces with other 
> tools which all have gff's that can be loaded into the ucsc genome browser.
> is there a conversion between the miso summary file and a gff?
> Thanks in advance,
> Maayan
> 
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