Question: How to filter out the non-coding genes?
0
gravatar for liux.bio
5.3 years ago by
liux.bio340
China
liux.bio340 wrote:

Hi,

Biostars. I have a list of genes with Ensembl gene ids and I want to filter out non-coding genes and  get protein-coding genes. I am using Bioconductor package BiomaRt, but can't find a direct way. Any suggestions?  

Many thanks!

bioconductor genome • 1.8k views
ADD COMMENTlink modified 16 days ago by Scott McKay10 • written 5.3 years ago by liux.bio340

Can you use the R script you used to figure this out? I am trying to do something similar now and am having trouble.

ADD REPLYlink written 16 days ago by Scott McKay10
2
gravatar for Prakki Rama
5.3 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:

I used Transcript Biotype in the attribute to check if it is actually protein coding or not. It seems pretty straightforward using Biomart.

ADD COMMENTlink written 5.3 years ago by Prakki Rama2.3k

Got it. Thank you!

ADD REPLYlink written 5.3 years ago by liux.bio340
0
gravatar for Scott McKay
16 days ago by
Scott McKay10
Scott McKay10 wrote:

Can you post the R script you used to figure this out? I am having a terribly hard time trying to do something similar here.

ADD COMMENTlink written 16 days ago by Scott McKay10

Use the biomaRt vignette. If you have ids as ensembl gene ids it is pretty easy. Let x be a character array with your ensembl gene ids (with and without version information)

goids = getBM(attributes = c('ensembl_gene_id', 'gene_biotype'), 
              filters = 'ensembl_gene_id', 
              values = x, 
              mart = ensembl)

Below is the information for gene biotypes.

https://useast.ensembl.org/info/genome/genebuild/biotypes.html

Also I think you should add your post as comment rather than answer.

ADD REPLYlink written 16 days ago by piyushjo170
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