Tutorials for Genomics
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,...
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...
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...
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...
In this case study, I attempted to improve on the draft assembly of a bacterial genome by combining the original and new data, and using new bioinformatics tools that have become available since we first assembled the genome and...