[miso-users] exon-centric analysis

[mali salmon]

Thanks Yarden for your reply
One more question. I have downloaded mm9 exonic-events gff file from your
site. The uncompressed folder contains few gff files + ensGene.map and
locuslink.map folders.
Can you please explain the content of these two folders? which one is the
indexed folder? Shall I index each gff file separately?
I have tried to run
"run_events_analysis.py --compute-genes-psi mm9 input.bam --output-dir
output --read-len 36" but this command yield nothing, so I suppose the
problem is with the indexing (I haven't run index_gff.py, assuming the
folder downloaded from your site is "ready to use")
Thanks
Mali


On Mon, Apr 23, 2012 at 1:28 AM, Yarden Katz <yarden at mit.edu> wrote:

> Hi Mali,
>
> see replies below:
>
> On Apr 22, 2012, at 2:33 AM, mali salmon wrote:
>
> > Hello MISO users
> > Two questions:
> > 1. I have BAM files generated using Tophat that was given a RefSeq GFF
> as input. Now I would like to do an exon-centric analysis using the ensembl
> gff file provided in MISO.
> > Is it a problem that the mapping was done with refseq annotations and
> not Ensembl?
>
> You can use any annotation with MISO -- the only requirement is that the
> chromosome naming schemes in your BAM file match the chromosome naming
> scheme in your GFF file.  See note on this here:
> http://genes.mit.edu/burgelab/miso/docs/#human-mouse-gene-models-for-isoform-centric-analyses
>
> > 2. Before I'm writing it myself,  is there a script provided for
> generating exon-centric gff based on isoform-centric gff files?
> > Thanks
> > Mali
> >
>
> There is not generic a script that takes isoforms and converts them into
> events.  There are many ways to go about generating distinct types of
> events (SE, AFE, ALE, ...) that require decisions to be made about what
> counts as SE versus A3SS, etc.
>
> You can either write a script that makes these categorizations based on
> rules that you find reasonable.  If you're using Drosophila, mouse or human
> genomes, you can instead use the event annotations that we provide.  The
> mapping from isoforms to events is complex and so there are many reasonable
> ways of doing it -- the events we provide are just one annotation.
>
> Hope this helps.
>
> Best, --Yarden
>
>
>
>
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