ROLLUP_DOC: how is this defined?

LANL-Bioinformatics / GOTTCHA

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Please visit our homepage:

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ROLLUP_DOC: how is this defined? #11

Closed donovan-h-parks closed 6 years ago

donovan-h-parks commented 6 years ago

Hello,

I couldn't find an explanation for ROLLUP_DOC and am curious how this is calculated. It appears to be the recommended method for using GOTTCHA at this point so am interested in how it differs from LINEAR_DOC.

Thanks, Donovan

poeli commented 6 years ago

Hello Donovan,

ROLLUP_DOC is the summation of average depth of coverage of unique signature length of each strain belonging to this taxonomy ( Σ_i=strains ( TOTAL_BP_MAPPED_i / unique_signature_length_i) ).

We found ROLLUP_DOC can represent abundance better since LINEAR_DOC over calculates abundance in some cases like stacking reads in a short region.

I am closing this issue for now. You are welcome to reopen it if you have any other questions.

Thanks, Paul