search

arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
318 stars 118 forks source link

gemini pathways will not work with non-Ensembl transcript IDs #258

Open lbeltrame opened 10 years ago

lbeltrame commented 10 years ago

As the KEGG pathways are mapped to Ensembl transcript IDs, any other ID for transcript (example: RefSeq) will fail the checks in the tool, and nothing will be outputted.

This can be inconvenient for data which is annotated against non-Ensembl provided genomes, such as UCSC's hg19.

udp3f commented 10 years ago

The protein level annotation that is supported in GEMINI is exclusively for ensembl genes/transcripts as both VEP and snpEFF annotations are based on these. Like wise, the pathways are mapped to these transcripts only. We have no support for RefSeq transcripts in GEMINI?

lbeltrame commented 10 years ago

snpEff can also use hg19 (which I need to use due to the way my experiments are set up). That said, if there's a format for these files, I'm betting they could be regenerated very easily for RefSeq (and if so, I could do that).

udp3f commented 10 years ago

I see! Probably linking the pathway files to refseq transcripts should help then.

Sent from my iPhone

On Jan 30, 2014, at 4:18 AM, "Luca Beltrame" notifications@github.com<mailto:notifications@github.com> wrote:

snpEff can also use hg19 (which I need to use due to the way my experiments are set up). That said, if there's a format for these files, I'm betting they could be regenerated very easily for RefSeq (and if so, I could do that).

— Reply to this email directly or view it on GitHubhttps://github.com/arq5x/gemini/issues/258#issuecomment-33671301.