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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:22] – [Importing data into Qiime2] bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/23 09:15] – [Qiime2 data filtering and feature (OTU) table construction] bngina
@@ Line 30: / Line 30: @@
 </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 view the imported data;
+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;
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  --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]].
+Important to keep in mind is the size of the amplified region covered by the primers used and what is the expected fragment length after read joining? This will determine the trim and truncate length parameters for dada2 and deblur pipelines.