[miso-users] RE : How to get isoform ID in the output file

[Delong, Zhou]

Hello,
Thanks for the reply.
I checked my annotation files and they are indeed v2.0 Gff files from the website, the file sizes matches.
Is there an option I'm missin in the command line? 
Thanks,
Delong

________________________________________
De : Yarden Katz [yardenny at gmail.com] de la part de Yarden Katz [yarden at mit.edu]
Envoyé : 31 août 2013 19:30
À : Delong, Zhou
Cc : miso-users at MIT.EDU
Objet : Re: [miso-users] How to get isoform ID in the output file

Hi,

There's a mapping from event names to gene IDs in the v2.0 GFF files (http://genes.mit.edu/burgelab/miso/docs/annotation.html).

Best, --Yarden

On Aug 30, 2013, at 2:37 PM, Delong, Zhou wrote:

> Hello,
> I used miso with human genome annotations provided by the miso webpage and I am wondering if I can have gene name / isoform ID instead of positions of each exon as identification of events.
> For instance here is an example of output:
>
> Event name: chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-
> Isoforms: 'chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-.A.dn_chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-.A.se_chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-.A.up','chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-.B.dn_chrUn_gl000223:98910:99036:- at chrUn_gl000223:98546:98641:- at chrUn_gl000223:93510:95942:-.B.up'
>
> I'd like to map this to an UCSC annotation or ensembl id. Does miso have an option to do that?
> Thanks,
> Delong
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