qiime tools import   --type EMPSingleEndSequences   --input-path emp-single-end-sequences   --output-path emp-single-end-sequences.qza

#use no golay error correction flag (golay error correction in reverse reads only)
qiime demux emp-single   --i-seqs emp-single-end-sequences.qza   --m-barcodes-file ovex_mapping_sham_ovex_sample_removed.tsv  --m-barcodes-column BarcodeSequence --p-no-golay-error-correction  --o-per-sample-sequences demux.qza   --o-error-correction-details demux-details.qza

qiime demux summarize   --i-data demux.qza   --o-visualization demux.qzv

#trim primers and truncate at 240 for quality
qiime dada2 denoise-single   --i-demultiplexed-seqs demux.qza   --p-trim-left 22   --p-trunc-len 240  --p-n-threads 8 --o-representative-sequences rep-seqs-dada2.qza   --o-table table-dada2.qza   --o-denoising-stats stats-dada2.qza

qiime feature-table summarize  --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file ovex_mapping_sham_ovex_sample_removed.tsv

qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv

qiime phylogeny align-to-tree-mafft-fasttree --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs.qza --o-masked-alignment masked-aligned-rep-seqs.qza --o-tree unrooted-tree.qza --o-rooted-tree rooted-tree.qza

qiime diversity core-metrics-phylogenetic   --i-phylogeny rooted-tree.qza   --i-table table.qza   --p-sampling-depth 9638   --m-metadata-file ovex_mapping_sham_ovex_sample_removed.tsv   --output-dir core-metrics-results

qiime diversity alpha-rarefaction   --i-table table.qza   --i-phylogeny rooted-tree.qza   --p-max-depth 9638   --m-metadata-file ovex_mapping_sham_ovex_sample_removed.tsv   --o-visualization alpha-rarefaction.qzv

qiime feature-classifier classify-sklearn --i-classifier gg-13-8-99-515-806-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza

qiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file ovex_mapping_sham_ovex_sample_removed.tsv --o-visualization taxa-bar-plots.qzv


#export phylogenetic tree and taxonomy file for import into phyloseq
qiime tools export --input-path rooted-tree.qza --output-path tree/

qiime tools export --input-path taxonomy.qza --output-path taxa/

biom convert -i merged.otu.sham.ovex.txt -o table.sham.ovex.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy

biom convert -i exported-features/feature-table.biom -o exported-features/otu_table_sham_ovex.txt --to-tsv