Question: Converting .fasta files to .gff3 files
0
gravatar for chenbenyuan
2.2 years ago by
chenbenyuan0 wrote:

I'm trying to use Roary to do phylogenetic analysis.

It says "Alternatively you can use ncbi-genome-download to pull down the FASTA files and convert them to GFF3 with Prokka." in https://sanger-pathogens.github.io/Roary/

I already have all the .fasta file I need.

How am I supposed to convert it to .gff3 files?

Thank you.

roary gff3 fasta • 2.1k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.2 years ago by chenbenyuan0

Roary manual states that you can use Prokka to convert fasta to .gff3

ADD REPLYlink written 2.2 years ago by Sej Modha4.1k
1
gravatar for sysbiocoder
2.2 years ago by
sysbiocoder170
sysbiocoder170 wrote:
  1. Convert fasta to BED first Check this How Do I Convert Fa Files To Bed Format? for that
  2. use gff-tools (http://www.raetschlab.org/suppl/gff-tools) to convert BED to gff3
ADD COMMENTlink written 2.2 years ago by sysbiocoder170
1
gravatar for jrj.healey
2.2 years ago by
jrj.healey11k
United Kingdom
jrj.healey11k wrote:

Prokka is a genome annotation pipeline. You aren't 'converting' the fasta as such. It's just the input to prokka which then adds all the annotations and features required.

Prokka then outputs various fasta files as well as a GFF3 and GBK.

You can then use those GFF3s as Roarys input.

I suggest you download and read the manual for prokka by Torsten Seemann

ADD COMMENTlink written 2.2 years ago by jrj.healey11k
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