[miso-users] exon-centric analysis

[Yarden Katz]

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