Hello everyone!
I have some MAGs and predictions from Prokka, which I used for KofamScan. Now I want to cluster those gene names into pathways. It looks like KEGGDecoder is the right tool.
I have a question. The output from KofamScan looks like this:# gene name KO thrshld score E-value KO definition
#-------------------- ------ ------- ------ --------- ---------------------
* PROKKA_00001 K00304 111.17 115.8 5.1e-34 sarcosine oxidase, subunit delta [EC:1.5.3.24 1.5.3.1]
PROKKA_00001 K22085 112.40 85.3 9.2e-25 methylglutamate dehydrogenase subunit B [EC:1.5.99.5]
So, if I am not mistaken, I need to filter them using one of these criteria - thrshld, score, or E-value - before processing further.
Which one should I use: thrshld, score, or E-value?
Thanks! Maybe someone can suggest different tools or approaches. I would appreciate any help.
Best