Tutorials for Genomics
There are many ways to compare genomes, and these comparisons provide different kinds of information about evolutionary history and shared function. First, how do you decide which genes are “the same” across multiple genomes,...
Why use Prokka? First, because in a benchmark test it has been shown to be as or more accurate at reproducing known annotation than RAST or xBASE2 in most annotation categories. Second, because it’s...
Genome browsers are designed to get different types of genome track data together using the common reference system of genomic coordinates. Often you’re more interested in manipulating whole sets of data, rather than just...
For today’s class, I have prepared a shared dropbox folder that contains the following items: sequence reads from one of the better chloroplast genome samples generated with our Ion Torrent instrument ERR008613 (a set...
DNA Sequencing is a continually evolving technology, with new platforms becoming available each year, all designed with the aim of reducing the cost and increasing the speed of large sequencing projects. As you can...
Many of the assignments in BINF 6203 are scaled so that you can complete them on a reasonably powerful laptop without using the University Research Computing cluster. That said, in order to do the...
Like last week’s tutorial, this tutorial uses Urban Environmental Genomics Project data. The original version of the tutorial was developed by Anju Lulla for our student interns. Preparation and software installation MetaPhlAn can be...
This tutorial makes use of the data from the NC Urban Microbiome Project, a collaboration seeded by the Department of Bioinformatics and Genomics and involving participants from our department as well as Civil Engineering,...
This lab takes us back to the tomato chloroplast genome data again. You’ve QCed the chloroplast data, assembled it, mapped it, used it to learn genome track math with bedtools, and produced a consensus...
With many thanks to Anju Lulla — this is a modification of a protocol she used for the paper we are working on with our collaborators. To start off this lab, you should have...
