Extracting genomic feature sequences from GTF/GFF files with AGAT

Tutorial:Extracting genomic feature sequences from GTF/GFF files with AGAT

20

Entering edit mode

19 months ago

Juke34 7.3k

First install AGAT:

conda create -c bioconda -n agat agat 
conda activate agat

Then enjoy possibilities of agat_sp_extract_sequences.pl, below exemplified

enter image description here

GFF corresponding to the record used as reference: enter image description here

extract GTF GFF sequence • 3.0k views

ADD COMMENT • link updated 11 weeks ago by eggrandio ▴ 40 • written 19 months ago by Juke34 7.3k

1

Entering edit mode

A great toolkit in Perl, kudos for that!

ADD REPLY • link 19 months ago by Michael Dondrup 52k

0

Entering edit mode

I assume this retrieves the sequence, but I was wondering if it's possible to retrieve an annotated version of the sequence, for example, in Genbank format, where the introns and exons are mapped. I would find that extremely useful.

By the way. thank you for creating AGAT, it has saved me many headaches when using GFF files!

ADD REPLY • link 11 weeks ago by eggrandio ▴ 40

Login before adding your answer.