V4_classifier.md

V4 amplicons

Extracting V4 region

Primers: 515f & 806r

qiime feature-classifier extract-reads --i-sequences silva138_noEuk_AB_seqs_uniq.qza --p-f-primer GTGYCAGCMGCCGCGGTAA --p-r-primer GGACTACNVGGGTWTCTAAT --p-n-jobs 12 --o-reads silva138_AB_V4seqs.qza

Output: silva138_AB_V4seqs.qza

Dereplicating the target region

qiime rescript dereplicate --i-sequences silva138_AB_V4seqs.qza --i-taxa silva138_noEuk_AB_tax_uniq.qza --o-dereplicated-sequences silva138_AB_V4seqs_uniq.qza --o-dereplicated-taxa silva138_AB_V4taxa-uniq.qza --p-threads 12

Dereplicated Sequences: silva138_AB_V4seqs_uniq.qza
Dereplicated Taxa: silva138_AB_V4taxa-uniq.qza

Classifying & evaluating with RESCRIPt

Using multiple threads increases memory usage Ref. Tried and sticking with 1 thread and using --p-reads-per-batch option (took approx 24 hrs)

qiime rescript evaluate-fit-classifier --i-sequences silva138_AB_V4seqs_uniq.qza --i-taxonomy silva138_AB_V4taxa-uniq.qza --p-reads-per-batch 10000 --o-classifier silva138_AB_V4_classifier.qza --o-observed-taxonomy silva138_AB_V4_predicted_taxonomy.qza --o-evaluation silva138_AB_V4_classifier_eval.qzv

Classifier: silva138_AB_V4_classifier.qza
Predicted Taxonomy: silva138_AB_V4_predicted_taxonomy.qza
Evaluation: silva138_AB_V4_classifier_eval.qzv