Question: List of Ensembl Transcript IDs corresponding to protein-coding genes
1
gravatar for Kristin Muench
3.3 years ago by
United States
Kristin Muench410 wrote:

Hello,

Does anyone know where I can find a list of Ensembl transcript IDs (e.g., ENST0000011111) associated with protein-coding genes?

I've run my mRNA-Seq data through kallisto and am plotting PCA on the pseudocounts, which are associated with Ensembl Transcript IDs. A labmate wonders if my PCA would cluster better if I only used the rows of counts corresponding to Ensembl Transcript IDs associated with mRNA (since, presumably, all of the other rows would be 0, since the sequencing was only done on mRNA, not ncRNA).

I'm not sure to what extent removing rows of 0s would change my PCA, but I thought I'd give it a try.

Thanks for your help!

rna-seq pca ensembl • 2.3k views
ADD COMMENTlink modified 3.3 years ago by EagleEye6.2k • written 3.3 years ago by Kristin Muench410
4
gravatar for mehran.karimzade
3.3 years ago by
Canada
mehran.karimzade150 wrote:

Go to:

http://www.ensembl.org/biomart/martview/21893b6a5bf91112c9a786f296b9200d

Choose database > Ensembl Gene 83 > Homo sapiens

Attributes > Gene > click on Ensembl Protein ID (or any other protein IDs such as refseq, etc.)

go to results and download

 

ADD COMMENTlink written 3.3 years ago by mehran.karimzade150
0
gravatar for EagleEye
3.3 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Use GTF from ensembl 

ftp://ftp.ensembl.org/pub/release-83/gtf/homo_sapiens

ADD COMMENTlink written 3.3 years ago by EagleEye6.2k
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