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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 18:02]
bngina [Qiime2 data filtering and feature (OTU) table construction]
population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 18:09] (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
  
-#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.txt · Last modified: 2020/04/29 18:09 by bngina