results of gene detection with the doublepass option

[rubmc97]

Hi,

So I ran SqueezeMeta to analyse several metagenomes and to retrieve ARGs, including the doublepass option (--D). I was wondering if for the downstream analyses of the ARGs I should consider only the ORFs detected with blastx (blastx as method on table 13) or both (the ones which contain either prodigal or blastx in method in the output table 13)? I went through the instructions .pdf but I'm not entirely sure on how to proceed.

Many thanks,
Ruben Martinez

[fpusan]

Hi,
You should in principle use both. Blastx may catch some extra genes that were not predicted by prodigal.