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caozhichongchong / arg_ranker

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Can the files from the pipeline ARGs_OAP V2.0 directly be used in arg_ranker? #3

Closed chunxiao-dcx closed 2 years ago

chunxiao-dcx commented 2 years ago

Dear authors: Can the files from the pipeline ARGs_OAP V2.0 directly be used in arg_ranker? We found some related describtion in the previous version. "3. Run\ arg_ranker -f True -fo output_dir\ arg_ranker -i formated_table.normalize_cellnumber.gene.tab -m metadata.txt " But the command could not be found in the new version. and it is quite blurry. When we tried to use"arg_ranker -i extracted.fa.normalize_cellnumber.gene.txt -m meta_data_online.txt", blank result was out put

caozhichongchong commented 2 years ago

Hi,

Thank you for your question. No, arg_ranker only works for ARGs_OAP V1.0.

The previous version was designed as a downstream analysis for ARGs_OAP V1.0. The newest version incorporated ARGs_OAP V1.0 into arg_ranker, directly evaluating ARG risk based on sequences.

Hope it helps!

Best regards, Anni

caozhichongchong commented 2 years ago

Hi,

I have noticed an error of arg_ranker.v2 when reporting the total ARG abundance in metagenomes. If the total ARG abundance is used in your research, please refer to https://github.com/caozhichongchong/arg_ranker for more details! I'm really sorry about this inconvenience! Please feel free to reach out to me if you have any questions.

Best regards, Anni

chunxiao-dcx commented 2 years ago

您好，您的邮件已收到，会尽快给您回复的~ 谢谢。