Question: Selecting One Ensembl Transcript Id For Each Ensembl Gene Id
3
gravatar for jackuser1979
5.2 years ago by
jackuser1979830
US
jackuser1979830 wrote:

I have transcript assembly and I have tried to annotate to human Ensembl cDNA through tblastx. I got blast top hits in Ensembl transcript id. I have converted these top hits Ensembl transcript id to Ensembl Gene id through Biomart tool. But now I have many transcripts match to same gene. If I have to consider one transcript for each gene what criteria can I choose? Whether based on transcript length or any other criteria?

For eg

Ensembl Gene ID     Ensembl Transcript ID
 ENSG00000139618     ENST00000380152
 ENSG00000139618     ENST00000530893
 ENSG00000139618     ENST00000528762
 ENSG00000139618     ENST00000470094
 ENSG00000139618     ENST00000533776
 ENSG00000139618     ENST00000544455

In the above example which Ensembl transcript id can I choose for the gene ENSG00000139618?

ensembl conversion • 2.0k views
ADD COMMENTlink modified 4 weeks ago by Astrid_Ensembl70 • written 5.2 years ago by jackuser1979830
3

The answer to your question lies in what you need to accomplish. Just think of it this way: if you selected one at random would that be acceptable? If not then why?, With that you have the rule by which to select your transcript.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Istvan Albert ♦♦ 74k
2

why not simply keep the best hit from Blast? For each sequence you can assign only the best Ensemble transcript ID

ADD REPLYlink written 5.2 years ago by JC6.3k

Thanks for reply. How can I choose representative transcript for a gene. So, can I select one at random? or should go for selecting best transcript for a gene based on transcript length, no.of exons predicted for that transcript?

ADD REPLYlink written 5.2 years ago by jackuser1979830
0
gravatar for gaoteng
4 weeks ago by
gaoteng10
gaoteng10 wrote:

I recently ran in to the same problem. You can use Transcript Support Level given by Ensembl and the transcript length to decide which transcript is "canonical" (somewhat subjectively). I wrote a script that achieves this: https://github.com/teng-gao/genomics_utils

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by gaoteng10
1

To enlarge your answer, the APPRIS annotation is also a very good indicator to select transcripts with several isoforms. :)

ADD REPLYlink written 4 weeks ago by glihm530
0
gravatar for Astrid_Ensembl
4 weeks ago by
EMBL-EBI
Astrid_Ensembl70 wrote:

There is a (relatively new) Ensembl training video on YouTube on the topic of 'Choosing a transcript':

https://www.youtube.com/watch?v=v-e93gJCV2c

ADD COMMENTlink modified 4 weeks ago by Istvan Albert ♦♦ 74k • written 4 weeks ago by Astrid_Ensembl70
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