population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/28 10:45] – bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 14:23] – [Importing data into Qiime2] bngina | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== Analysis of Microbiome data ====== | ====== Analysis of Microbiome data ====== | ||
- | Micriobial analysis aims to understand microbes and their functions in their environments. [[https:// | + | Micriobial analysis aims to understand microbes and their functions in their environments. [[https:// |
+ | |||
+ | We outline a pipeline to analyse 16S/18S paired-end sequencing data. Qiime2 can be used to analyse single-end and paired-end data. | ||
+ | |||
+ | ==== Importing data into Qiime2 ==== | ||
+ | |||
+ | [[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:// | ||
+ | |||
+ | Read more about [[ https:// | ||
+ | |||
+ | To import fastq files; | ||
+ | |||
+ | < | ||
+ | |||
+ | #i create a directory to store all my artifact i.e ' | ||
+ | |||
+ | mkdir / | ||
+ | |||
+ | #import the fastq files | ||
+ | |||
+ | qiime tools import \ | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, | ||
+ | |||
+ | < | ||
+ | |||
+ | qiime demux summarize \ | ||
+ | | ||
+ | | ||
+ | </ |
population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina