[miso-users] Identifying novel isoforms

[Yarden Katz]

Hi Warren,

MISO does not provide transcript assembly / annotation.  For that, I recommend looking into a transcript assembly tool like Scripture.  Any transcript annotation tool can output a format like GFF (or one easily convertable to GFF) which you can then use with MISO for quantitation and/or plotting with sashimi plot.

We're currently working on a new pipeline for annotation alternative events that will take as input the kinds of formats produced by transcript assembly programs, and from them derive a set of event annotations (i.e. a categorization of skipped exons, retained introns, and so on.)  You might be interested in these scripts as well when they are released.

Best, --Yarden


On Oct 23, 2012, at 12:16 PM, Warren Emmett wrote:

> Hi,
> 
> I have been looking through the miso manual, I'm not sure if its possible to visualise and identify novel isoforms that are not present in the gff annotation from ensembl ? Is there a command to let you create an annotation from the bam file?
> 
> Thanks
> Warren 
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