Sequence Read QC
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...
Category: genomics
Prepare Your Computer
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...
BINF 6203: 16S rRNA classification with QIIME
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,...
BINF 6203: Read Mapping
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...
BINF 6203: Bacterial genome annotation with prokka
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...
UEGP: Detecting antibiotic resistance determinants
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...
Summer Research: Urban Environmental Genomics Project
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...
BINF 2111: Exploring SNPs with bedtools (Lab)
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...
BINF 2111: Assembly at the Command Line (Lab)
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...
Sidebar: DE with Tuxedo pipeline #usegalaxy
To get around the problems with the software installs in the lab (and that some of you are having installing corset on your own) here is another way to get a full DE gene...