[miso-users] miso error

[mykhwab]

Thanks Yarden,,

one another thing,
there is a statement that
IGV <http://www.broadinstitute.org/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
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>
>
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