Tutorials for Genomics
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...
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...
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,...
Mapping short sequence reads to a reference sequence is a common task in genomics. Many different results can be extracted from a mapped sequence, depending on the original experimental design that produced the sequence...
In previous iterations of this course, we’ve used the RAST/SEED servers to perform annotation. RAST is a highly regarded genome annotation pipeline, and you will easily be able to justify using it to reviewers...
One of the main sequence analysis tasks we want to perform on the UEGP dataset is the evaluation of antibiotic resistance potential in the wastewater microbial community. We have examples of analytical approaches to this...
This summer, my students and I are working through analysis of wastewater microbiome sequencing data. The analysis includes 3 timepoints, 11 sampling points, 2 wastewater treatment streams, and 3 replicates of each sample. 198 samples...
We’re not quite ready to launch into full-on python scripting just yet — so here’s a little add-on to your final bash project, to help make use of the output files you generate. Why...
Today’s lab task is preparation for developing a script that will assemble a batch of small genome sequence data sets. In our script development process there are four main steps: Figure out the pipeline...