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GhMathis / oracle

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majority assignation "metagenome" in taxonomical level (from class to species) #4

Open GhMathis opened 1 month ago

GhMathis commented 1 month ago

For the bacteria majority assignation (didn't check for fungi) : I've detected 1202 OTU that have "metagenome" as taxonomical assignation. Can we change that or it is an error from the database ?

GhMathis commented 1 month ago

@frederic-mahe in "Oracle_soils_16S_341F_785R_87_samples.OTU.filtered.cleaved.nosubstringOTUs.mumu.table2"

frederic-mahe commented 1 month ago

Some reference sequences in GenBank, and in Silva (8,862 entries), were obtained from "metagenomes" (see for example NFZJ01010884). We could exclude these reference sequences, but our environmental sequences would then be assigned to more distant references, or would not be assigned at all.