Question: Convert Cds-Based Coordinate To Genomic Coordinates
2
gravatar for Luca Beltrame
5.5 years ago by
Luca Beltrame210
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
Luca Beltrame210 wrote:

I was given a list of loci of interest for a particular gene, which contain mutations: unfortunately, all the information are using local base coordinates, while I'm in need to retranslate them to genomic coordinates to perform some additional work in preparation for validation. I've seen a few example of genomic -> local coordinate transformation, but not the opposite.

Bear in mind that I have access to the whole annotation of the genome (Homo sapiens), so using additional files and/or resources wouldn't be a problem.

Is there a way to convert from local coordinates to genomic coordinates? Python or R solutions would be preferred.

genome mapping • 3.5k views
ADD COMMENTlink modified 5.5 years ago by Emily_Ensembl18k • written 5.5 years ago by Luca Beltrame210

which organism ?

ADD REPLYlink written 5.5 years ago by Pierre Lindenbaum120k

It's Homo sapiens.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Luca Beltrame210

Is this the problem where you have variants reported on transcript level like g.195insCTGATA in RB1 gene? Having the same problem here... I am looking forward to Pierre's solution

ADD REPLYlink written 5.5 years ago by Irsan6.8k

More like genomic sequence (all the coordinates are mapped to the canonical variant of the gene), but yes, something like that.

ADD REPLYlink written 5.5 years ago by Luca Beltrame210
3
gravatar for Emily_Ensembl
5.5 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

Ensembl REST API. Scroll down to Mapping to see tools to get genomic coordinates from cDNA, CDS and protein coordinates. Since it's a REST API, you can use it in your favourite language.

ADD COMMENTlink written 5.5 years ago by Emily_Ensembl18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1940 users visited in the last hour