Select only protein coding Ensembl ID

Question

[sumitguptabt]

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

Answer 1

[Kevin Blighe]

Hi,

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

Kevin

[sumitguptabt]

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