Too many resistance gene from RGI bwt

[pratibha-kadam]

Dear developers,

This is just to increase my understanding on the resistance genes from CARD database.

I have downloaded the latest RGI 6.0.3 and I have run RGI bwt as I have the wastewater data from Illumina. I am getting 4500 ARGs as an output for each sample.

When I did the co-occurance analysis of bacterial taxa found from Kraken2, and ARG genes from RGI, I am getting 2.5M correlations of bacteria and ARG based on spearman rank correlation. Even though if I filter the correlation data based on correlation >0.9 and p value <0.01, 2500000 significant correlations remain.

I want to know is there any way to reduce the ARG based on some criteria or only focus on significant genes.

[github-actions]

Issue is stale and will be closed in 7 days unless there is new activity