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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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What does the unnormalized file actually contain? #28

Open alanxelena opened 1 year ago

alanxelena commented 1 year ago

Hi!

First of all, thanks for this tool! I've been using the normalized tables so far so I have never really paid attention to the unnormalized files but now I'm trying to get something that is not normalized. The numbers in these files confuse me a little, what do they mean? I guess they're not counts since I have values like 0.03 but I also assume they are not percentages since I also have values of 132.472. Any help would be really appreciated!!

xinehc commented 1 year ago

Hi,

unnormalized copies are computed for each gene using sum(aligned length/gene length). The results are further aggregated to three different levels so you see three different files in the output folder. Note that for short-read the values should be very similar to sum((subject start - subject end)/subject length) considering each gene as a subject.

unnormalized count are counts of reads aligned to each gene (aggregated using the same way as before).

HTH, Xi

alanxelena commented 1 year ago

Thanks! that answers a lot of things! I have another issue this time but I'll post it separately.

Thanks again!