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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 13:44] – bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:49] – bngina
@@ Line 13: / Line 13: @@
 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//.
-Import data as follows:
+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/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>
+==== Qiime2 data filtering and feature (OTU) table construction ====
+Qiime2 provides two pluggins/methods for filtering your sequences to the required quality and length and from these construct featuretables better known as OTU tables and the representative feature sequences. These are [[https://www.ncbi.nlm.nih.gov/pubmed/27214047| Dada2]] and [[ https://msystems.asm.org/content/2/2/e00191-16| Deblur]].