population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data
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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 11:50] – bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 15:02] – [Qiime2 data filtering and feature (OTU) table construction] bngina | ||
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=== Dada2 === | === Dada2 === | ||
- | The Dada2 pipeline detects and corrects illumina amplicon sequence data and additionally | + | The Dada2 pipeline detects and corrects illumina amplicon sequence data and additionally |
To see usage and parameters that can be adjusted get the help for the pluggin i.e | To see usage and parameters that can be adjusted get the help for the pluggin i.e | ||
Line 54: | Line 54: | ||
</ | </ | ||
- | The data we are using is paired-end hence we will use the < | + | The data we are using is paired-end, hence we will use the [[https:// |
+ | A key parameter to be careful about is the //'' | ||
+ | |||
+ | The other key parameters in quality control of the sequences are those used to trim the forward, '' | ||
+ | |||
+ | To determine what values to pass for these two parameters; | ||
+ | *Review the Interactive Quality Plot tab in the //'' | ||
+ | *The expected fragment size after the reads are joined, particularly for the //'' | ||
+ | |||
+ | The command would therefore be | ||
+ | |||
+ | < | ||
+ | qiime dada2 denoise-paired \ | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
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+ | #next summarise the features table and view, | ||
+ | | ||
+ | time qiime feature-table summarize \ | ||
+ | | ||
+ | | ||
+ | |||
+ | |||
+ | #view a summary of the rep sequences | ||
+ | |||
+ | time qiime feature-table tabulate-seqs \ | ||
+ | | ||
+ | | ||
+ | |||
+ | #and also view the denoising statistics | ||
+ | time qiime metadata tabulate \ | ||
+ | --m-input-file ${data_dir}/ | ||
+ | --o-visualization ${qzv_dir}/ | ||
+ | </ |
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina