[ensembl-dev] transcript coordinates via REST?

[Andrew Yates]

> On 12 Aug 2015, at 19:26, Reece Hart <reece at harts.net> wrote:
> 
> On Mon, Aug 10, 2015 at 6:30 AM, Andrew Yates <ayates at ebi.ac.uk <mailto:ayates at ebi.ac.uk>> wrote:
> What we are really getting to here is the difference between using the genome as a scaffold to build annotation on from primary data alignment versus projecting known sequence annotation onto the genome. As you have suggested there will be cases where the genome does not represent the RefSeq annotation accurately and so alignment files are necessary. The GENCODE transcripts represent a best attempt at constructing a valid model on the genome and so transcript sequence and genome are in agreement. 
> 
> Right. I think we've had a similar view throughout the exchange.

I think we have

> 
> Clinical literature is built up around specific transcripts. It's terrific when a clinical area happens to use a GENCODE transcript, but that's not always a case. (ALMS1 being one example of that.)

We do realise that GNECODE annotation will not be used by some clinical groups. We are always working towards the best and most comprehensive annotation possible and will continue to do so.

Cheers

Andy

> 
> Thanks,
> Reece
> 
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