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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/28 11:14] – bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 13:52] – [Importing data into Qiime2] bngina
@@ Line 8: / Line 8: @@
 [[https://docs.qiime2.org/2020.2/concepts/|Data]] used and produced by qiime2 are stored as artifacts. Artifacts contain data and metadata and have a ''.qza'' extension. Qiime2 provides methods to view information (data and metadata) stored in artifacts by creating visualizations, that have a ''.qzv'' extension.
+We import raw fastq files into qiime2. Depending on the sequencing platform used to generate the data, you will have data that has been de-multiplexed into sample specif fastq files, or not. The MiSeq platform at [[ https://hub.africabiosciences.org/| BecA-ILRI Hub]] will de-multiplex the data and we get sample specific fastq files.
+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 artefact i.e '.qza' and the related visualizations 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>