How can I get the list of all human ensembl transcript ids?

I am trying to create a small local database consisting of all human grch38 ensembl transcript IDs and their sequences. I can get the sequences using biomaRt in R, but how can I get all the human transcriptIDs?

ensembl

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updated 1.9 years ago by Louisse_Ensembl •

• written 1.9 years ago by ramiro.barrantes •

1 answer

you can use the ENSEMBL gtf file and if you want to make a txdb, take a look at https://rdrr.io/bioc/GenomicFeatures/man/makeTxDbFromGFF.html

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written 1.9 years ago by Ming Tommy Tang

GTF files can be found on the Ensembl FTP site at https://ftp.ensembl.org/pub/current_gtf/homo_sapiens/

Cheers, Louisse (Ensembl Helpdesk)

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written 1.9 years ago by Louisse_Ensembl •

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