How to filter out resistance genes in metagenomics?

[mhmism]

Hello,

Thank you for this amazing tool and your continuous maintenance and support.

I ran rgi bwt on some human shotgun metagenomics samples. I would like to know how to filter out the gene output file to avoid false positives. For example, should I keep only identified genes with 100% Average Percent Coverage and remove the rest? If only a few samples show one or two genes with 100% Average Percent Coverage and the rest none, can I stretch this percent a bit to include more genes in more samples?

Are there any other parameters or cut-off values that I should keep in mind before doing the downstream analyses in my samples?

Many thanks in advance! any help or guidance will be appreciated.

Kind regards Mahmoud