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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 13:48] – bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:23] – [Importing data into Qiime2] bngina
@@ Line 17: / Line 17: @@
 <code>
-#i create a directory to store all my ''.qza'' artefact and the related visualizations i.e ''.qzv''.
+#i create a directory to store all my artifact i.e '.qza' and the related visualization i.e '.qzv' files.
+mkdir /home/mydir/qiime2_data/
+#import the fastq files
 qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
- --input-path /home/bngina/Fellows/Yves_Tchiechoua/orig_data \
+ --input-path /home/mydir/qiime2_data/ \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
- --output-path /home/bngina/Fellows/Yves_Tchiechoua/qiime2_data/yves_data1.qza
+ --output-path /home/mydir/qiime2_data/my_raw_data.qza
+</code>
+We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, .qzv, files. The ''.qzv''  files can be opened on any browser using [[https://view.qiime2.org/ |qiime viewer]]. To create visualization for the imported data;
+<code>
+qiime demux summarize \
+ --i-data  /home/mydir/qiime2_data/my_raw_data.qza \
+ --o-visualization /home/mydir/qiime2_data/my_raw_data.qzv
 </code>