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

[Yarden Katz]

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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