Do we have Hits data from the output txt?

[Former user]

Dear Resfinder Team,

I'm currently running run_resfinder.py for my gut microbiome fastq files for detecting the ARGs from mobile genetic elements. I got these results from run_resfinder.py:

➜ test_output l total 204K drwxrwxr-x 3 xmixu xmixu 10 Dec 6 00:42 . drwxrwxr-x 7 xmixu xmixu 7 Dec 6 00:21 .. -rw-rw-r-- 1 xmixu xmixu 5.6K Dec 6 00:42 pheno_table.txt -rw-rw-r-- 1 xmixu xmixu 15K Dec 6 00:42 ResFinder_Hit_in_genome_seq.fsa drwxrwxr-x 2 xmixu xmixu 70 Dec 6 00:42 resfinder_kma -rw-rw-r-- 1 xmixu xmixu 14K Dec 6 00:42 ResFinder_Resistance_gene_seq.fsa -rw-rw-r-- 1 xmixu xmixu 1.7K Dec 6 00:42 ResFinder_results_table.txt -rw-rw-r-- 1 xmixu xmixu 794 Dec 6 00:42 ResFinder_results_tab.txt -rw-rw-r-- 1 xmixu xmixu 48K Dec 6 00:42 ResFinder_results.txt -rw-rw-r-- 1 xmixu xmixu 25K Dec 6 00:42 std_format_under_development.json

But I didn't find the hits number of the ARGs. Do we have hits data for these ARGs from mobile genetic elements?

Best regards,

Xinming

[CGE Helpdesk]

Dear Xinming,

Thank you for your interest in ResFinder.
ResFinder can be used to identify AMR genes in a sample but cannot tell where these are located. To investigate this I would recommend to use another CGE service https://cge.cbs.dtu.dk/services/MobileElementFinder/.

Best,
Karen, CGE Helpdesk