Question: How To Get Ensembl Id (Gene, Transcript, Protein) Information?
1
gravatar for mgab
3.1 years ago by
mgab40
Germany
mgab40 wrote:

I have few VCF Files which contains Chromosome number, position, Variation allele (Ref and Alt).

How can I generate the Gene name, its Refseq and listing all of its transcripts? 1. Any tool which gives these kind of results when upload VCF data? 2. Is there any module in Biopython or Bioconductor or script for this? 3. Is there any lists that links gene name to Refseq and transcript information?

Thank you for the valuable suggestions

ensembl transcripts python R exome • 1.6k views
ADD COMMENTlink modified 3.1 years ago by Emily_Ensembl18k • written 3.1 years ago by mgab40
4
gravatar for memory_donk
3.1 years ago by
memory_donk230
Australia
memory_donk230 wrote:

Ensembl BioMart is probably your best bet.

You may need to use/write a quick script or awk command to extract your chromosome number and position but you can enter a list of chromosomal positions in the filter menu under regions->multiple chromosomal positions. You can then choose which attributes you would like to download such as Ensembl Gene ID or (under the external references menu) Refseq id.

If your list is too long you'll probably have to use the Perl API. Short tutorial available here: http://www.ensembl.org/info/data/biomart/biomart_perl_api.html

ADD COMMENTlink written 3.1 years ago by memory_donk230

Thank you for donk for the suggestion

ADD REPLYlink written 3.1 years ago by mgab40
4
gravatar for Emily_Ensembl
3.1 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

You need the variant effect predictor, does exactly what you need.

ADD COMMENTlink written 3.1 years ago by Emily_Ensembl18k

Thank you for Emily for the suggestion

ADD REPLYlink written 3.1 years ago by mgab40
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