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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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ARG-OAP Output file explaination #39

Open pratibha-kadam opened 1 year ago

pratibha-kadam commented 1 year ago

Hello There,

  1. I have little doubt about normalized_16s.gene.txt/normalised_16s.subtype.txt/normalised_16s.type.txt The gene names which I can are ARG genes, so, can u just breif me about the 16s files. I thought it will include data bacterial species from which ARG detected.

and, also what are the normalised.cell.*.txt files?

  1. I want to include bedauiline as a drug in the database can you please help me where I can get the sequence of ARG genes. The genes are atpE,Rv0678,pepQ. Its not in there in any ARG databases.

Thanks in advance ;)

xinehc commented 1 year ago

hi,

I have little doubt about normalized_16s.gene.txt/normalised_16s.subtype.txt/normalised_16s.type.txt The gene names which I can are ARG genes, so, can u just breif me about the 16s files. I thought it will include data bacterial species from which ARG detected.

ARG copies are normalised by 16S copies in those files.

I want to include bedauiline as a drug in the database can you please help me where I can get the sequence of ARG genes. The genes are atpE,Rv0678,pepQ. Its not in there in any ARG databases.

I don't know where you can get the sequence, you may give NCBI protein/nucleotide a try.