Category: genomics

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...

Prepare Your Computer

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: 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...

UEGP: Detecting antibiotic resistance determinants

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

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)

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)

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

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...