[ensembl-dev] transcript coordinates via REST?

[Reece Hart]

On Mon, Aug 10, 2015 at 6:30 AM, Andrew Yates <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.

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.)

Thanks,
Reece
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