how to get transcript.fasta from gff file

Question

[evelyn]

Hello,

I got genome.fasta and gff files from a collaborator and I need a transcript.fasta for same genome. Is it possible to get it from the available files. Thank you in advance!

Answer 1

[GenoMax]

You can use gffread (LINK).
AGAT toolkit may also have this functionality.

[Juke34]

Here some example how to use agat_sp_extract_sequences.plfrom AGAT to extract whatever you need: Extracting genomic feature sequences from GTF/GFF files with AGAT

Answer 2

[lieven.sterck]

getfasta from bedtools should (could) also work.

but also a +1 for AGAT ;)