Hi, I am conducting a meiofauna analysis in beach sand. I have 192 samples. My samples were sequenced using the primers 18S F04mod: GCTTGWCTCAAAGATTAAGCC and R22mod: CCTGCTGCCTTCCTTDGA. I used the silva-138-99-nb-classifier.qza classifier from the resources page, and when I examine the taxonomy file, I get these strange results in some classifications:
d__Eukaryota;p__Peronosporomycetes;c__Peronosporomycetes;o__Peronosporomycetes;f__Peronosporomycetes d__Eukaryota;p__Labyrinthulomycetes;c__Labyrinthulomycetes;o__Labyrinthulomycetes;f__Thraustochytriaceae;g__Aplanochytrium;s__ . . . It seems that names belonging to groups are assigned as phylum. Is this normal? Is there any way to correct it?
I have also used a custom classifier using RESCRIP as follows:
qiime rescript get-silva-data \
--p-version '138.1' \
--p-target 'SSURef_NR99' \
--o-silva-sequences silva-138.1-ssu-nr99-rna-seqs.qza \
--o-silva-taxonomy silva-138.1-ssu-nr99-tax.qza
qiime rescript reverse-transcribe \
--i-rna-sequences silva-138.1-ssu-nr99-rna-seqs.qza \
--o-dna-sequences silva-138.1-ssu-nr99-seqs.qza
qiime rescript cull-seqs \
--i-sequences silva-138.1-ssu-nr99-seqs.qza \
--o-clean-sequences silva-138.1-ssu-nr99-seqs-cleaned.qza
qiime rescript filter-seqs-length-by-taxon \
--i-sequences silva-138.1-ssu-nr99-seqs-cleaned.qza \
--i-taxonomy silva-138.1-ssu-nr99-tax.qza \
--p-labels Eukaryota \
--p-min-lens 1400 \
--o-filtered-seqs silva-138.1-ssu-nr99-seqs-filt.qza \
--o-discarded-seqs silva-138.1-ssu-nr99-seqs-discard.qza
qiime rescript dereplicate \
--i-sequences silva-138.1-ssu-nr99-seqs-filt.qza \
--i-taxa silva-138.1-ssu-nr99-tax.qza \
--p-mode 'uniq' \
--o-dereplicated-sequences silva-138.1-ssu-nr99-seqs-derep-uniq.qza \
--o-dereplicated-taxa silva-138.1-ssu-nr99-tax-derep-uniq.qza
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads silva-138.1-ssu-nr99-seqs-derep-uniq.qza \
--i-reference-taxonomy silva-138.1-ssu-nr99-tax-derep-uniq.qza \
--o-classifier silva-138.1-ssu-nr99-uniq-classifier.qza
And I get the same results.
This is my first time using qiime2 and I am not very familiar with it yet, so I don't know if this is normal or if I am making a mistake.