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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 13:57] – [Qiime2 data filtering and feature (OTU) table construction] 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]] method of the pluggin.
+A key parameter to be careful about the //''--p-trunc-q''//, which is basically a Q-score value. The default is a Q-score of 2, which means that in filtering for quality while reading the sequence from left to right, as soon as it encounters a base with a Q-score lower that threshold, by default its set to 2, the read is truncated at that position
+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.