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transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
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Combine step 5 outputs from different samples #71

Open Vincev454 opened 2 years ago

Vincev454 commented 2 years ago

Hi everyone,

Is there a way (a script?) to combine all Refseq or subsystem outputs from step 5 in order to get only one table combining the result of ALL samples?

Thanks in advance for your input, Vince

transcript commented 2 years ago

Hey Vince!

I don't have a script to combine all of the step 5 outputs, but it should be fairly straightforward to do. I'd throw out the percentage column and just use the raw counts column, and then merge by substance or function name.

I could probably throw a script together for this next week, or feel free to look into it yourself and offer an option/pull request.

Best, Sam