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

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 sRNAanno database

srna
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updated by TerryDDiaz • TerryDDiaz • written by r00628112 • r00628112

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?

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written by barslmn • barslmn

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

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written by r00628112 • r00628112

1 answer

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

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written by Juke34 Juke34

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