Ensembl equivalent of refseq transcript fasta

Question

[Jalil Sharif]

Hello,

I am trying to find the newest human grch38 transcriptome fasta file. On refseq, the latest can be accessed here - https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_rna.fna.gz

However, I want the latest by ensembl and I am not sure what the exact link is for that one as there are few to choose from here:

https://www.ensembl.org/info/data/ftp/index.html

[Marco Pannone]

Do you need the latest Ensembl .gtf file for transcriptome annotation? If so: https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/

[Jalil Sharif]

And is there a way to change the gtf file to a fasta file, so I can use it for alignment?

Answer 1

[GenoMax]

You can find the Ensembl equivalent at this link: https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/cdna/ Take a look at the README file to check what is included.

You may also want to look at the MANE project which is a collaboration between NCBI/EBI.

[Jalil Sharif]

great thanks