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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:01] – [Qiime2 data filtering and feature (OTU) table construction] bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:09] (current) – [Qiime2 data filtering and feature (OTU) table construction] bngina
@@ Line 68: / Line 68: @@
 <code>
 qiime dada2 denoise-paired \
- --i-demultiplexed-seqs ${data_dir}/armel_run2.qza \
+ --i-demultiplexed-seqs /home/mydir/qiime2_data/my_raw_data.qza \
  --p-trim-left-f 0 \
  --p-trim-left-r 0 \
  --p-trunc-len-f 250 \
  --p-trunc-len-r 220\
- --o-table ${data_dir}/armel_run2_dada2_470_table.qza \
+ --o-table /home/mydir/qiime2_data/dada2_470_table.qza \
- --o-representative-sequences ${data_dir}/armel_run2_dada2_470_rep-seqs.qza \
+ --o-representative-sequences /home/mydir/qiime2_data/dada2_470_rep-seqs.qza \
- --o-denoising-stats ${data_dir}/armel_run2_dada2_470_denoising-stats.qza \
+ --o-denoising-stats /home/mydir/qiime2_data/dada2_470_denoising-stats.qza \
  --p-n-threads 4
+#summarise the features table to view it,
+qiime feature-table summarize \
+ --i-table /home/mydir/qiime2_data/dada2_470_table.qza \
+ --o-visualization /home/mydir/qiime2_data/dada2_470_table.qzv
+#view a summary of the rep sequences
+qiime feature-table tabulate-seqs \
+ --i-data  /home/mydir/qiime2_data/dada2_470_rep-seqs.qza \
+ --o-visualization  /home/mydir/qiime2_data/dada2_470_rep-seqs.qzv
+#and also view the denoising statistics
+qiime metadata tabulate \
+  --m-input-file /home/mydir/qiime2_data/dada2_470_denoising-stats.qza \
+  --o-visualization /home/mydir/qiime2_data/dada2_470_denoising-stats.qza
 </code>