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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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How to filter out resistance genes in metagenomics? #148

Closed mhmism closed 1 year ago

mhmism commented 3 years ago

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

raphenya commented 1 year ago

@mhmism setting cutoff depends on your data. For example, you would not want to rely on 100% Average Percent Coverage if a lot of the reads are covering part of a particular gene. Hope that helps. Cheers.