[miso-users] miso error

[Yarden Katz]

To plot this, you have to use sashimi_plot:

http://genes.mit.edu/burgelab/miso/docs/sashimi.html 

We've been working with IGV to get something like sashimi_plot implemented in the IGV browser.  Not sure when this feature will come out, but it's on the list.

  --Yarden


On Dec 25, 2012, at 8:35 PM, mykhwab wrote:

> Thanks Yarden,,
> 
> one another thing, 
> there is a statement that 
> IGV: Visualizer of mapped reads (e.g. BAM files). Displays junction reads.
> 
> is there any option in MISO for doing so, just like mention in the example plots on web..
> 
> 
> Regards 
> 
> On Tue, Dec 25, 2012 at 11:26 PM, Yarden Katz <yarden at mit.edu> wrote:
> It's a warning and it's normal in most cases, just signaling that it is not indexing genes with only 1 transcript/mRNA.  Those genes by definition have no alternative regions, and so there's no use in quantifying their isoform abundances.
> 
>   --Yarden
> 
> On Dec 25, 2012, at 8:49 AM, mykhwab wrote:
> 
> >
> >
> >
> > Hi
> >
> > after running this command
> >
> >       python index_gff.py --index SE.gff3 indexed_SE_events/
> >
> > I have got thtis error..the program is skipping some genes. Why is this so, how can i fix it?
> >
> >
> >
> >
> > Cannot make gene out of AT5G66890
> > WARNING: AT5G66900 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66900
> > WARNING: AT5G66910 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66910
> > WARNING: AT5G66920 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66920
> > WARNING: AT5G66940 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66940
> > WARNING: AT5G66950 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66950
> > WARNING: AT5G66960 does not have at least two mRNA/transcript entries with exons. Skipping over...
> > Cannot make gene out of AT5G66960
> > WARNING: AT5G66970 does not have at least two mRNA/transcript entries with exons. Skipping over...
> >
> >
> >
> > Regards
> >
> >
> > _______________________________________________
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> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
> 
> 
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