Extracting genomic feature sequences from GTF/GFF files with AGAT

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

21

Entering edit mode

3.0 years ago

Juke34 8.5k

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 • 5.8k views

ADD COMMENT • link updated 19 months ago by eggrandio ▴ 40 • written 3.0 years ago by Juke34 8.5k

1

Entering edit mode

A great toolkit in Perl, kudos for that!

ADD REPLY • link 3.0 years ago by Michael 54k

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 19 months ago by eggrandio ▴ 40

Login before adding your answer.