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

First install AGAT:

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

Then enjoy possibilities of agat_sp_extract_sequences.pl, below exemplified

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

extract gtf gff sequence
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updated by eggrandio • eggrandio • written by Juke34 Juke34

A great toolkit in Perl, kudos for that!

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written by Michael Dondrup Michael Dondrup

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!

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written by eggrandio • eggrandio

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