[miso-users] Events with many gene annotations

[Sol Katzman]

Dear Yarden and Tyler,

A while back, I noticed some performance problems processing AFE/ALE events.

I extracted the distributions of the lengths of the "gene" items in the gff3
(hg19) event definitions. There are many (1100+/500+) AFE/ALE events over 1Mb in length.
Only a handful (10) such SE events.

I will send my stats in a follow-up email.

I think that the events longer than 1Mb are pretty questionable.

/Sol.

On 8/28/2013 2:16 PM, Tyler Funnell wrote:
> Hi Yarden,
>
> Yes that's right. The problem is most noticeable for the ALE/AFE events for the reason you mentioned, but I think the current event to gene mapping could have improper annotations for other event types as well. For example, small genes that exist within the introns in a SE event would be picked up.
>
> Cheers,
> Tyler
>
>
> On Aug 28, 2013, at 2:03 PM, Yarden Katz <yarden at mit.edu> wrote:
>
>> 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
>>
>
>
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users
>