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--- population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 13:07] – bngina
+++ population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 14:36] – [Qiime2 data filtering and feature (OTU) table construction] bngina
@@ Line 54: / Line 54: @@
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-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.
+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.
-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.
+A key parameter to be careful about is the //''--p-trunc-q''//, which is a Q-score value. This means that in filtering for base 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.Be careful with this, best to leave it at the default.
+The other 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.
+To determine the truncate length, look at the imported reads, t