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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 detection in a species genome #12

Open qutkat opened 2 weeks ago

qutkat commented 2 weeks ago

Hello, Just trying to figure out how I could use omixer to detect the presence of GBMs in a particular species. If I was just looking to produce the coverage file could I load a table with the KOs present in the species genome as opposed to the sample metagenome? Would it work if I just included presence/absence data (0/1) as opposed to abundances of the KOs within the genome?

Thanks,

Katherine

omixer commented 2 weeks ago

Hi Katherine,

Presence/absence data would work here as well. For instance, a module with 4 steps out of 5 are present will have a coverage of 80% with abundance or presence/absence data. If the module coverage cutoff is set at 70%, the module will be present. If it is set at 100% the module will be absent.

Hipe this helps