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 [2020/03/28 11:28] – bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:49] – bngina | ||
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We import raw fastq files into qiime2. Depending on the sequencing platform used to generate the data, you will have data that has been de-multiplexed into sample specif fastq files, or not. The MiSeq platform at [[ https:// | We import raw fastq files into qiime2. Depending on the sequencing platform used to generate the data, you will have data that has been de-multiplexed into sample specif fastq files, or not. The MiSeq platform at [[ https:// | ||
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+ | Read more about [[ https:// | ||
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+ | To import fastq files; | ||
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+ | < | ||
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+ | #i create a directory to store all my artifact i.e ' | ||
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+ | mkdir / | ||
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+ | #import the fastq files | ||
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+ | qiime tools import \ | ||
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+ | </ | ||
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+ | We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, | ||
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+ | < | ||
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+ | qiime demux summarize \ | ||
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+ | </ | ||
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+ | ==== Qiime2 data filtering and feature (OTU) table construction ==== | ||
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+ | Qiime2 provides two pluggins/ | ||
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population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina