By default, VEP uses the Ensembl/GENCODE transcript set when analysing your variants, but you can also choose to use NCBI’s RefSeq transcripts.
Continue readingCool stuff the Ensembl VEP can do: analysis with RefSeq transcripts
Tag: RefSeq
RefSeq column returning for GRCh37
Following the response to our switch to the new RefSeq Match column in the transcript tables, we have reverted the tables on GRCh37 back to the old style. The table now lists the RefSeq column as before. We apologise for any confusion this has caused.
We are making ‘MANE’ changes…
The RefSeq column on our gene pages has changed.
We’re moving towards a more unified gene-set with RefSeq, with biologically important transcripts being highlighted as MANE. This means displays you’re used to seeing will be updated to reflect these changes, and this may affect the way you have been working with Ensembl.
Coming soon! MANE Select v0.5
Joannella Morales, Jane Loveland and Adam Frankish contributed to this post.
Back in October, we introduced you to our new joint initiative with the NCBI — the Matched Annotation from the NCBI and EMBL-EBI (MANE) transcript set. We are now pleased to update you on our progress so far.
The goal of this project is to share annotation and converge on a high-confidence, genome-wide transcript set, with a matched transcript in both RefSeq and Ensembl/GENCODE. We are doing this in two phases. During phase 1, we will release the “MANE Select” transcript set to include one well-supported transcript for every protein-coding locus. We envision the adoption of the MANE Select set as a default set across genomics resources. In phase 2, we intend to release an expanded set (“MANE Plus”) to include additional transcripts per locus that are well-supported or of particular user interest.
Our new joint transcript initiative : The Matched Annotation from the NCBI and EBI (MANE) project
This blog post is a joint contribution by Joannella Morales, Jane Loveland, Adam Frankish, Fiona Cunningham and Astrid Gall.
We are pleased to introduce the Matched Annotation from the NCBI and EMBL-EBI (MANE) project. This new joint initiative between EMBL-EBI’s Ensembl project and NCBI’s RefSeq project aims to release a genome-wide transcript set that contains one well-supported transcript per protein-coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl (ENST) transcript.
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