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raeslab / omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
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The input file data format is not accepted. #10

Closed suyouR closed 2 weeks ago

suyouR commented 5 months ago

Hi! After I used HUMAnN3 to annotate the metagenome, I obtained two formats of KO annotation results: one is presented in the form of RPK (reads per kilobase), the other is relative abundance data after the RPK data is normalized. I tried to use relative abundance data to run Omixer-RPM using the [GMM Database], but there were no results. I would like to know whether I can use relative abundance data to run, and how should I convert my data to meet the right format?

omixer commented 5 months ago

Hi @suyouR,

You can use the relative abundance or the RPKs but please make sure they are formatted correctly, and as described here https://github.com/raeslab/omixer-rpm?tab=readme-ov-file#input-file-format.

Best regards, Youssef