[ensembl-dev] Ensemble GRCh38 Transcript ID

[Pankaj Agarwal]

Thank you for providing this clarification.  I had just a couple of quick follow up questions.
These ids came out of Ensembl Transcript fasta file (Homo_sapiens.GRCh38.cdna.all.fa) which I used for the first time in rna-seq data analysis.  Earlier I had been using the GTF file which probably does not have the version id
1. Is there a function with in biomart or any Ensembl tool to remove the version numbers from a list of transcript ids.
and/or
2. Is there a way to get a mapping from the Transcript IDs to Gene Names that will circumvent the issue of version id.
Thanks,
- Pankaj


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Matthew Laird
Sent: Wednesday, December 21, 2016 8:02 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Ensemble GRCh38 Transcript ID

Hello Pankaj,

Those are version numbers, they've been a part of Ensembl stable ids since the start but not always displayed in every context, you can read more about the rules for how they're incremented here:

http://www.ensembl.org/info/genome/stable_ids/versions.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.org_info_genome_stable-5Fids_versions.html&d=CwMD-g&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=IDwpe2wIkw9bdBMqeNsKTRZmbtvkqETUeUnJsNoNd4E&m=3TZBnak0YkbHUaCUhR7sPjdI-kpwbMFVh7Ug_Jtzc8w&s=0dbfmrUnD3j-2gUyaMXfTEYB4CkonFKwa6fSyHhZBR4&e=>

Biomart does not accept versioned stable ids in queries, if you're submitting a batch of stable ids to Biomart you must ensure they are unversioned.

Cheers.
On 21/12/16 12:52, Pankaj Agarwal wrote:
Hi,
The Ensembl Transcript IDs for the GRCh38 version has periods at the end followed by a number.  For ex:
ENST00000414852.1
ENST00000390399.3
ENST00000610439.4
When I query these in biomart it does not work.  I have remove the period and the following number.
I was wondering why these were introduced, what they mean, and how to get these to work with Biomart.
Thanks,
- Pankaj
-----------------------------
Pankaj Agarwal, M.S
Bioinformatician
Data Analyst
Applied Therapeutics
Div. of Surgical Sciences
Dept. of Surgery
Duke University
M: 919-244-6389
O: 919-681-2251
p.agarwal at duke.edu<mailto:p.agarwal at duke.edu>





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