Question: Can Orthofinder produce FastA?
0
gravatar for bsp017
2.0 years ago by
bsp01730
Denmark, Copenhagen, UCPH
bsp01730 wrote:

Is it possible to get a FastA file of orthologs using Orthofinder? I ran orthofinder (v2.2.7) like this:

orthofinder.py -f sane_files/ -t 40 -M msa

I got around 9000 orthogroups from my genomes. I would like to Blast these against some databases e.g. CAZy database. But I need a FastA file.

Thanks,

James

ADD COMMENTlink written 2.0 years ago by bsp01730
1

Would the following option be relevant in your case?

os               Stop after writing sequence files for orthogroups
                   (requires '-M msa')
ADD REPLYlink written 2.0 years ago by Sej Modha4.7k

Adding that command gives the proteins that make up the orthogroup. I was wanting a single consensus sequence for each orthogroup. Not sure if there is an easy way to do that? For example, I got 9000 orthogroups, so I wanted a FastA file with 9000 proteins.

ADD REPLYlink written 2.0 years ago by bsp01730
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