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Question: How to convert Bed, or GFF3 files to fasta?
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gravatar for ricfoz
12 months ago by
ricfoz • 0
ricfoz • 0 wrote:

Hello everyone, i am new to the bioinformatic world, and i am trying to do a phylogeny with a gene. I am retrieving the sequences from different organisms, being some of those neandertal sequences, which i happen to download from a genome browser. These sequences are in GFF3 format, but i need to transform them to a .fasta file so i can run the phylogeny algorithm on them. Browsing through galaxy i have managed to convert them to BED format, i thought that could be an intermediate step in order to convert them to fasta, but i am stuck there.

Any suggestions on how to transform GFF3 files to fasta in galaxy?, thanks in advance and greetings to the community.
galaxy • 1.4k views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by ricfoz • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

Please see the tool: Extract Genomic DNA

The input is a BED/GTF/GFF dataset. The output is fasta sequence or interval format that includes the sequence.

A custom genome can be used whenever the target genome is not included on the server. https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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