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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data

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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:01]
bngina [Qiime2 data filtering and feature (OTU) table construction]
population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:09] (current)
bngina [Qiime2 data filtering and feature (OTU) table construction]
Line 68: Line 68:
 <code> <code>
 qiime dada2 denoise-paired \ 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-f 0 \
  --p-trim-left-r 0 \  --p-trim-left-r 0 \
  --p-trunc-len-f 250 \  --p-trunc-len-f 250 \
  --p-trunc-len-r 220\  --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  --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> </code>
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.1588172492.txt.gz · Last modified: 2020/04/29 15:01 by bngina