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How to extract sequence of a specific feature in gff

I have a gff file like this:

Bany_Scaf24 maker   gene    41357   46444   .   +   .   ID=Bany_09696;Name=Bany_09696;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0;
Bany_Scaf24 maker   mRNA    41357   46444   .   +   .   ID=Bany_09696-RA;Parent=Bany_09696;Name=Bany_09696-RA;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=277|1|1|1|0|0|2|35|76;_eAED=0.00;score=1829;
Bany_Scaf24 maker   exon    46189   46444   .   +   .   ID=Bany_09696-RA:1;Parent=Bany_09696-RA;
Bany_Scaf24 maker   exon    41357   41643   .   +   .   ID=Bany_09696-RA:2;Parent=Bany_09696-RA;
Bany_Scaf24 maker   five_prime_UTR  41357   41633   .   +   .   ID=Bany_09696-RA:five_prime_utr;Parent=Bany_09696-RA;
Bany_Scaf24 maker   CDS 41634   41643   .   +   0   ID=Bany_09696-RA:cds;Parent=Bany_09696-RA;
Bany_Scaf24 maker   CDS 46189   46409   .   +   2   ID=Bany_09696-RA:cds;Parent=Bany_09696-RA;
Bany_Scaf24 maker   three_prime_UTR 46410   46444   .   +   .   ID=Bany_09696-RA:three_prime_utr;Parent=Bany_09696-RA;
B

I also have the genome fasta file. How do I generate two fasta files of 'gene' and 'three_prime_UTR' based on the the coordinates?

rna-seq gff genome assembly
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updated by Juke34 Juke34 • written by tianshenbio tianshenbio

1 answer

Yes you can definitely do it with agat_sp_extract_sequences.pl from AGAT
e.g for three_prime_UTR feature:
agat_sp_extract_sequences.pl --gff input.gff --fasta input.fasta -t three_prime_UTR

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written by Juke34 Juke34

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