Assign taxonomy DADA2

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1

Assign taxonomy

I use Dada2, R 363 and Dada 2 1.16 tutorial aiming to create OTU table of Illumina Miseq 16S rRNA sequences. The tutorial assign taxonomy command brings to the page below... I do not know what to read out... Eukaryotic sequences? while we studied the 16S sequence of bacteria. Something apparently went wrong in processing the data. Could you please give a hint?

head(track)
input filtered denoisedF denoisedR merged nonchim
TA-2423-Rhizo2Ser205-1-EKTO 88630 85678 72916 81381 18 18
TA-2423-Rhizo2Ser205-2-EKTO 109849 106941 91901 103048 3 3
TA-2423-Rhizo2Ser205-3-EKTO 94610 91885 77732 88214 20 20
TA-2423-Rhizo2Ser211-1-EKTO 81891 79259 62509 74931 28 28
TA-2423-Rhizo2Ser211-2-EKTO 98852 95893 80573 91586 21 21
TA-2423-Rhizo2Ser211-3-EKTO 90015 87377 70476 82730 7 7

taxa <- assignTaxonomy(seqtab.nochim,"~/EKTO/silva_nr_v138_train_set.fa.gz")
taxa <- addSpecies(taxa, "~/EKTO/silva_species_assignment_v138.fa.gz")
taxa.print <- taxa
rownames(taxa.print) <- NULL
head(taxa.print)
Kingdom Phylum Class Order Family Genus Species
[1,] "Eukaryota" NA NA NA NA NA NA
[2,] NA NA NA NA NA NA NA
[3,] "Eukaryota" NA NA NA NA NA NA
[4,] "Eukaryota" NA NA NA NA NA NA
[5,] "Eukaryota" NA NA NA NA NA NA
[6,] "Eukaryota" NA NA NA NA NA NA

2

Hi,

Since this question is a downstream issues from a questions posted elsewhere on this forum, we might wait answering this until the previous one has been resolved (which might fix this one too)

PJ

3

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