Dear Qiime community,
Finally, I reached the last step of my data analysis! I am performing a metagenomic study using four different primer pairs, and I have a little issue on the taxonomy result.
My question is about assign taxonomy to the representative OTU sequences. When I run the assing_taxonomy.py scrip with the blast option, for some of the samples I get the correct taxonomy assignment to the correspondent sequence of my database, but for some samples (sometimes are quite a lot of them), I don't get a taxonomy-sequence result, I just get as a result the name of the fasta database I used on this step with a number taht sometimes is the same but different in other otus (I have created my own database, which is a fasta file of a onw-curated collection of unique sequences. Not all the sequences on the reference database have the same lenght of my Illumina reads - for example, on the database I have sequences for the entire ITS region but I have only sequenced the ITS1 spacer).
I am a bit confused about what does it mean... I don't know if that is because the consensus sequence of this otu fits to more than one sequence of the database at the same time, and it cannot return a specific result.
Here is what I am talking about (see the otus 'denovo189, denovo370 and denovo430). Any idea of what does is it?
denovo748 Eukaryota Stramenopiles Oomycetes PeronosporalesPhytophthora PHYTOPHTHORA_TENTACULATA_CBS_41296_ITS 9 E-024 PHYTOPHTHORA_TENTACULATA_CBS_41296_ITS
denovo189 None 4 E-011 786_DBsingles.fasta
denovo370 None 0.000000003 786_DBsingles.fasta
denovo430 None 4 E-135 438_DBsingles.fasta
denovo438 Eukaryota Stramenopiles Oomycetes Peronosporales Phytophthora PD_00420_ITS_Phytophthora_taxon_Pgchlamydo 4E-051 PD_00420_ITS_Phytophthora_taxon_Pgchlamydo
Thanks a lot in advance!