list of all possible transcripts in ensembl format

Question

[anba]

Hi,

where can I find list of all possible transcripts (in ensembl format like ENST00000374811.8) with gene names?

[jkkbuddika]

Hi, I think you can gather the information you need from Ensembl annotations.

The following command should make a bed file with transcript information you need.

awk '$3 == "transcript"' Homo_sapiens.GRCh38.101.gtf > transcript_info.bed

Hope this helps.

KB

[Pierre Lindenbaum]

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

[jkkbuddika]

Biomart certainly is the better answer!

Answer 1

[ATpoint]

In R using biomaRt:

tx2gene <- mmusculus_genes <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "hgnc_symbol"),  
                                    mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl"))

head(tx2gene)

ensembl_transcript_id   ensembl_gene_id     hgnc_symbol
ENST00000387314         ENSG00000210049     MT-TF
ENST00000389680         ENSG00000211459     MT-RNR1
ENST00000387342         ENSG00000210077     MT-TV
ENST00000387347         ENSG00000210082     MT-RNR2
ENST00000386347         ENSG00000209082     MT-TL1
ENST00000361390         ENSG00000198888     MT-ND1

For mouse the dataset option would be mmusculus_gene_ensembl, for other organisms check the biomaRt/Ensembl documentation for the correct string. If there are empty slots for some of the HGNC symbol in the table then this not a bug, not every Ensembl gene ID has a matched HGNC (or in case of mouse MGI) symbol.