How to extract sequence in fasta format from micro RNA gff3 files (sRNAanno database)?

Question

[r00628112]

Dear all, I would like use the bulk miRNA data to do small RNA annotation, but sRNAanno database used gff3 format to storage sRNA information, May someone give a suggestion or solution to transform micro RNA gff3 file into fasta format?

Thank you very much

http://www.plantsrnas.org/software.html

[barslmn]

There are multiple ways of doing this that can be searched for using the search functionality. Explain more in details what is the output you want and what you tried?

[r00628112]

Thanks for your reply. I would like use fasta to do sRNA annotation

Answer 1

[Juke34]

If you have the genome fasta file and the gff3 you can use agat_sp_extract_sequence.pl from AGAT.