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raeslab / omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
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GBM module IDs #5

Closed hh1985 closed 3 years ago

hh1985 commented 3 years ago

Hi, @raeslab @omixer

Some GBM modules are mixed with different types of IDs, e.g.

134 MGB036  S-Adenosylmethionine (SAM) synthesis
135 K00789  TIGR01034   bactNOG02937

Just wonder what's the recommended way to utilize the module? Should I extract the sequences of each IDs into a fasta file, and mapped the reads into the sequences?

Thanks,

-Han

omixer commented 3 years ago

Hi @hh1985,

Before you can use the modules you have to generate a count table, for example by mapping your sequencing reads on a gene catalog like the IGC (https://db.cngb.org/microbiome/genecatalog/genecatalog_human/) which has KO annotation etc...

Once you have the table please refer to the README for generating module counts from the counts table!

Best regards, Youssef