Use of ORFs

[STabuteau]

Hi,

Thank you for your tool. I am currently using FeGenie on contigs and have tried to use it on ORFs as well. My results are quite different and those for ORFs are incoherent. I have the impression that in the current version, there is a problem with the use of ORFs. I just saw that you have put in your Upcoming Updates "the ability to accept previously annotated genomes and gene calls". Is this coming soon?

Thank you!

[ElsaMMendes]

Hi,

Me too I found there is a problem when using --orfs option ... if this option is used we obtain less results than if we don't use this option. When FeGenie doesn't launch Prodigal itself there is no clustering for exemple.

I'm using FeGenie 1.2 (last version)

[Arkadiy-Garber]

Hi! So sorry for letting these issues fall through the cracks. Thanks for your interest in FeGenie - and I hope you've been able to find your way around this issue.

using the --orfs flag will indeed cause FeGenie to skip the Prodigal step, precluding it from seeing gene proximities.

There is a hack that should allow you to trick FeGenie into accepting your pre-existing ORFs. This hack will only work if your ORFs are in the following format: CONTIG_NUM (where NUM is the numeric order of the ORF on the contig).

mkdir -p fegenie_out/ORF_calls
cp input_orfs/*faa fegenie_out/ORF_calls/
for i in fegenie_out/ORF_calls/*faa; do mv $i $i-proteins.faa; done
FeGenie.py -bin_dir input_orfs -bin_ext faa -out fegenie_out

This should trick FeGenie into using the ORFs that are copied into the fegenie_out/ORF_calls directory. Just be sure to answer 'y' when FeGenie asks if you're sure you want to use a pre existing output directory.

Hope this helps!
Arkadiy