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

[Yarden Katz]

Hi,

I'm not sure which option in the command line you're looking for.  The gene information is in the GFF file so you have to just parse that from the GFF file and use that in downstream analyses.  Since the MISO output files contain the event name, and the GFF contains gene information for each event, it's easy to match them up.  You have to do that as a post-processing step, it's not part of MISO.

best,  --Yarden



On Sep 3, 2013, at 9:40 AM, Delong, Zhou wrote:

> 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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>