Question

Select only protein coding Ensembl ID

0

Entering edit mode

3.5 years ago

sumitguptabt ▴ 30

Hi,

I wanted to use only protein-coding transcripts for RNAseq DE analysis using edgeR. Is there a way to select only protein-coding transcript ids? Some example data that I have:

ID Counts
ENSG00000000003 767
ENSG00000000005 16
ENSG00000000419 968
ENSG00000000003 767
ENSG00000000005 16

It would be really nice if I can also change the Ensembl id to Entrez id. Thank you in advance SK

R genes RNAseq EdgeR • 762 views

ADD COMMENT • link 3.5 years ago by sumitguptabt ▴ 30

score 3 · Accepted Answer · 2021-05-22

3

Entering edit mode

3.5 years ago

Kevin Blighe 88k

Hi,

Please take a look here, in particular, at the biomaRt answer: Translating gene names to entrez id's

Kevin

ADD COMMENT • link 3.5 years ago by Kevin Blighe 88k

1

Entering edit mode

Thank you Kevin Blighe, org.Hs.eg.db working perfectly. THanks SK

ADD REPLY • link 3.5 years ago by sumitguptabt ▴ 30