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

Question

[ramiro.barrantes]

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?

Answer 1

[Ming Tommy Tang]

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

[Louisse_Ensembl]

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

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Cheers, Louisse (Ensembl Helpdesk)