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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 13:26] – [Importing data into Qiime2] bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:20] – bngina
@@ Line 12: / Line 12: @@
 Read more about [[ https://docs.qiime2.org/2020.2/tutorials/importing/|different data types and importing them into qiime2]] for anlaysis. We will be importing data described as type //Cassava 1.8 paired-end de-multiplexed fastq//.
+To import fastq files;
+<code>
+#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/mydir/qiime2_data/ \
+ --input-format CasavaOneEightSingleLanePerSampleDirFmt \
+ --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. To view 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>