Hello everybody! 

I want to extract only mRNA from TxdB. So I did the following steps:

txdb <- makeTxDbFromGFF("Homo_sapiens.GRCh38.85.gtf", format="gtf" )
exonsByGene <- exonsBy(txdb, by="gene")

exonsByGene contains all exons including exons related to non-protein coding genes.

The question is how to subset exonsByGene to extract only mRNA (another words to take only exons that corresponds to protein coding genes)?

Thank you in advance!

Alex Gopanenko

Dear Alexandr,

it looks like your GTF is from Ensembl. In this case you might also try to use ensembldb and EnsDb databases instead of TxDb databases. With ensembldb you can then use filters to just extract the data you want. The workflow to generate the database is slightly different:

library(ensembldb)

## Create the database. Note that this creates the 
## SQLite database and does not return an EnsDb.
db <- ensDbFromGtf(gtf = "Homo_sapiens.GRCh38.85.gtf")

## Load this database
edb <- EnsDb(db)

## And use it: we'll use a GenebiotypeFilter to fetch
## only exons of protein coding genes

exonsByGene <- exonsBy(edb, filter = GenebiotypeFilter("protein_coding"), by = "gene")

While this returns all exons for all protein coding genes, it might still contain exons of non-coding transcripts of the protein coding genes, e.g. transcripts that are targeted for nonsense mediated mRNA decay.

cheers, jo