ILRI Research Computing

User Tools

Site Tools

You are here: start » population-diversity » microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data
population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Last revisionBoth sides next revision
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] bnginapopulation-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:02] – [Qiime2 data filtering and feature (OTU) table construction] bngina
Line 77: Line 77:
  --o-denoising-stats ${data_dir}/armel_run2_dada2_470_denoising-stats.qza \  --o-denoising-stats ${data_dir}/armel_run2_dada2_470_denoising-stats.qza \
  --p-n-threads 4  --p-n-threads 4
 +
 +#next summarise the features table and view, 
 +        
 +time qiime feature-table summarize \
 + --i-table ${data_dir}/armel_run2_dada2_470_table.qza \
 + --o-visualization ${qzv_dir}/armel_run2_dada2_470_table.qzv
 +
 +
 +#view a summary of the rep sequences
 +
 +time qiime feature-table tabulate-seqs \
 + --i-data ${data_dir}/armel_run2_dada2_470_rep-seqs.qza \
 + --o-visualization ${qzv_dir}/armel_run2_dada2_470_rep-seqs.qzv
 +
 +#and also view the denoising statistics
 +time qiime metadata tabulate \
 +  --m-input-file ${data_dir}/armel_run2_dada2_470_denoising-stats.qza \
 +  --o-visualization ${qzv_dir}/armel_run2_dada2_470_denoising-stats.qzv
 </code> </code>
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina