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Species cannot assigned to my data. Can anyone tell the problem?
```taxa <- assignTaxonomy(seqtab.nochim, refFasta = "/home/omic/Downloads/Final_analysis/fasta_files/rdp_train_set_18.fa.gz", minBoot = 80, tryRC = FALSE, outputBootstraps = FALSE, taxLevels = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), multithread = TRUE, verbose = TRUE)
taxa <- addSpecies(taxa, refFasta = "/home/omic/Downloads/Final_analysis/fasta_files/rdp_species_assignment_18.fa.gz", allowMultiple = FALSE, tryRC = FALSE, n = 2000, verbose = TRUE)
``` 0 out of 712 were assigned to the species level. Of which 0 had genera consistent with the input table.
@basketball legends So anyone have any suggestions?
You will get species level information if you remove primer sequences from your reads. I did that for my data then I got species level information. If you only remove adapter sequences then it might not work for you.
Thanks.