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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 15:02]
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]
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 <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
  
-#next summarise the features table and view, +#summarise the features table to view it
                  
-time qiime feature-table summarize \ +qiime feature-table summarize \ 
- --i-table ${data_dir}/armel_run2_dada2_470_table.qza \ + --i-table /home/mydir/qiime2_data/dada2_470_table.qza \ 
- --o-visualization ${qzv_dir}/armel_run2_dada2_470_table.qzv+ --o-visualization /home/mydir/qiime2_data/dada2_470_table.qzv
  
  
 #view a summary of the rep sequences #view a summary of the rep sequences
  
-time qiime feature-table tabulate-seqs \ +qiime feature-table tabulate-seqs \ 
- --i-data ${data_dir}/armel_run2_dada2_470_rep-seqs.qza \ + --i-data  /home/mydir/qiime2_data/dada2_470_rep-seqs.qza \ 
- --o-visualization ${qzv_dir}/armel_run2_dada2_470_rep-seqs.qzv+ --o-visualization  /home/mydir/qiime2_data/dada2_470_rep-seqs.qzv
  
 #and also view the denoising statistics #and also view the denoising statistics
-time qiime metadata tabulate \ +qiime metadata tabulate \ 
-  --m-input-file ${data_dir}/armel_run2_dada2_470_denoising-stats.qza \ +  --m-input-file /home/mydir/qiime2_data/dada2_470_denoising-stats.qza \ 
-  --o-visualization ${qzv_dir}/armel_run2_dada2_470_denoising-stats.qzv+  --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.1588172577.txt.gz · Last modified: 2020/04/29 15:02 by bngina