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Community Profile Analysis with Excel Pivot Tables
Community Profile Analysis with Excel Pivot Tables
Overview
Overview
A number of interesting and informative data visualizations of microbiome community profiles can be produced using Microsoft Excel Pivot Tables. The output OTU/ASV table produced by PUMAA is formatted for both Excel and STAMP analyses (Please note that OTU and ASV are used interchangeably in this manual).
Pivot tables are an excellent way to summarize the massive amounts of data in OTU/ASV tables into meaningful visualizations of the overall community profile of different samples at different taxonomic levels (phylum, class, order, family, genus, species). You can also make simple (non-statistical) comparisons of the abundances of OTUs/ASVs at different taxonomic levels.
Learning Objectives
Learning Objectives
Describe the pipeline of metagenomic sequence processing.
Analyze metagenomics data from microbial samples obtained from environmental sources.
Compare and contrast operational taxonomic units (OTUs) and amplicon sequence variants (ASVs).
Describe the components of an OTU or ASV abundance table.
Store and interrogate datasets using spreadsheets or delimited text files.
Evaluate different community profile visualization graphs.
How do we get from samples to an OTU or ASV file?
How do we get from samples to an OTU or ASV file?
Pivot Table Tutorials
Pivot Table Tutorials
PUMAA Manual Activity 1 (step by step written instructions with screenshots)
Slides with a step by step guide to Pivot tables (right).
Demo/Sample Data File
Demo/Sample Data File
See “EXCEL_community_demo.xlsx” for a formatted OTU/ASV pivot table with example data visualizations.
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