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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 10:14] – [Qiime2 data filtering and feature (OTU) table construction] bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 13:35] – bngina
@@ Line 50: / Line 50: @@
 To see usage and parameters that can be adjusted get the help for the pluggin i.e
+<code>
+qiime dada2 --help
+</code>
+The data we are using is paired-end, hence we will use the [[https://docs.qiime2.org/2020.2/plugins/available/dada2/|qiime dada2 denoise-paired]] pluggin.
+A key parameter to be careful is the //''--p-trunc-q''//
+Key parameters in quality control of the sequences are those used to trim the forward, ''--p-trim-left-f''; ''--p-trunc-len-f'' and reverse '' --p-trim-left-r''; ''--p-trunc-len-r'' reads. The //--p-trim-left-[f/r] tell qiime how many bases to trim from the beginning of the sequence, while the //--p-trunc-len[f|r] tell qiime at what position the sequences should be truncated at the end.