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...

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...

Under the hood: V. vulnificus JY1305

Under the hood: V. vulnificus JY1305

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...

Getting your 23 and Me data into Galaxy

Getting your 23 and Me data into Galaxy

I just happen to have a file with 960,628 lines of personal SNP data from 23 and Me burning a hole in my hard drive. I’m one of the lucky people who gets 23...

Getting your Galaxy to point to a working executable

Getting your Galaxy to point to a working executable

I’m running my own Galaxy and I want to use it to run the SPAdes assembler as part of a Galaxy pipeline, instead of running SPAdes at my command line with shell scripts. Ostensibly, this...

BINF 6215: Trinity and Corset at the command line

BINF 6215: Trinity and Corset at the command line

This tutorial is my version of the workflow for analysis of the Synechocystis PCC6803 gene expression data using Trinity and Corset. Disclaimer: walking through the workflow shows that there is plenty to be skeptical about in...