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 [2020/03/30 14:23] – [Importing data into Qiime2] bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 13:59] – [Qiime2 data filtering and feature (OTU) table construction] bngina | ||
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+ | ==== Qiime2 data filtering and feature (OTU) table construction ==== | ||
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+ | Qiime2 provides two pluggins/ | ||
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+ | 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. | ||
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+ | === Dada2 === | ||
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+ | The Dada2 pipeline detects and corrects illumina amplicon sequence data and additionally filter any phiX reads identified in sequencing data and also filter out any chimeric sequences. | ||
+ | To see usage and parameters that can be adjusted get the help for the pluggin i.e | ||
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+ | < | ||
+ | qiime dada2 --help | ||
+ | </ | ||
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+ | The data we are using is paired-end, hence we will use the [[https:// | ||
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+ | A key parameter to be careful about is the //'' | ||
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+ | The other key parameters in quality control of the sequences are those used to trim the forward, '' |
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina