[miso-users] Events with many gene annotations

[Yarden Katz]

Hi Tyler,

Some of the AFE/ALE annotations, which we are currently reworking, have span very large genomic coordinates as you noted.  I believe these are probably dubious/faulty annotations.  But in any case, as you say, if you overlap the outer-most coordinates with genes there will potentially be many overlapping genes.

If I understand correctly, you're proposing to merge the first exon with all genes, then the second exon will genes, and take the intersection of those? 

Best, --Yarden

On Aug 27, 2013, at 10:31 PM, Tyler Funnell wrote:

> Hello,
> 
> I've noticed that for some alternative events, there are many gene annotations in the event to ensembl Id mapping file. For example AFE event 83896 at uc002kgt.1@uc002hvt.1 has quite a few. I think this might be because the left-most and right-most coordinates for this particular event cover a large section of the chromosome and the gene mappings are based on these coordinates. If I'm right, I think a better way would be to get the overlap between genes (or gene exons) and individual event exons first, then merge to the event level.
> 
> Thank you,
> Tyler
> 
> 
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users