Bacterial metagenomics on the JHU campus: analyzing the data, part I

For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found.

Every year, I collect the data from her students' experiments. Then, in the bioinformatics classes I teach, we work with the chromatograms and other data to see what we can find.

This is the first part of a four part video series on using pivot tables to analyze the data.

This series covers:

I. Downloading the data from iFinch and preparing it for analysis. (this is the video below)

II. Cleaning up the data

III. Counting all the bacteria

IV. Counting the bacteria by biome

Through this work, we're trying to find identify the bacteria that live on the JHU campus and how those bacteria might be distributed in different environments. Since we have data from the past four years, we can also see if these results vary over time.

Part I. Pivot tables from Sandra Porter on Vimeo.

For information about this project, check here, here, here, and here.