Question: Getting CDS from chromosome positions
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gravatar for drmouradap
11 months ago by
drmouradap0
drmouradap0 wrote:

Hello! I'm sorry if this is a duplicate question. I've searched the forum and didn't find the answer to what I seek.

I'm working with exome sequencing data and some of the variants are not completely annotated. I have the chromosome positions of each variant, but not the CDS or protein change associated with it.

My question is how to extract the CDS from the chromosome positions of each variant, to translate these variants into Synonymous/Non-Synonymous variations and then get the predicted protein effects of each variant. I thought of using UCSC Genome Browser for that. I there an easy way to extract that information using Python?

Example: I want to get from chr9:34371171 T>C to c.T1773C / p.I591T.

ADD COMMENTlink modified 9 months ago by Luis Nassar410 • written 11 months ago by drmouradap0
2

. I've searched the forum and didn't find the answer to what I seek.

Tool for CDS Variants annotation : snpeff, vep, annovar, ...

ADD REPLYlink modified 11 months ago • written 11 months ago by Pierre Lindenbaum130k
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gravatar for JC
11 months ago by
JC11k
Mexico
JC11k wrote:

You can use Ensembl VEP API

ADD COMMENTlink written 11 months ago by JC11k
0
gravatar for Luis Nassar
9 months ago by
Luis Nassar410
UCSC Genome Browser
Luis Nassar410 wrote:

The UCSC Genome Browser may not be the most efficient tool to go from position coordinate to predicted effect via programmatic approach.

We recently announced our API (http://genome.ucsc.edu/goldenPath/help/api.html) which does allow python access to coding sequence given coordinates, as well as querying most of the available data (among other functions). Hopefully that will be of some use.

ADD COMMENTlink written 9 months ago by Luis Nassar410
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