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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...

BINF 2111: Genome Horoscope (eye color — part 2)

BINF 2111: Genome Horoscope (eye color — part 2)

Your mission for today is to write a script that checks a 23 and Me genotype file for several groups of SNPs that are associated with blue eyes. The SNPs in question are in...

BINF 2111: Genome Horoscope — eye color (Part 1)

BINF 2111: Genome Horoscope — eye color (Part 1)

In this week’s exercise, we’re going to practice loops and lists in Python by looping through a 23 and me file to pull out data that matches a list of SNPs of interest. Before...

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 6203: GAGE tutorial

BINF 6203: GAGE tutorial

This lab is offered as an opportunity for extra credit or for your project requirement (if applicable). This was presented by Dr. Luo during a guest lecture visit last year, so there is not...

BINF 6203: Expression Statistics

BINF 6203: Expression Statistics

Last week you used transcriptome and read mapping tools to get read counts for your Vibrio vulnificus expression data, with two different pipelines. Now let’s analyze the data and get the top differentially expressed...

BINF 6203: Gene expression read quantitation

BINF 6203: Gene expression read quantitation

In this lab and the next, we are going to use two different methods to calculate differential expression for the same RNASeq dataset. In a nutshell, we have measured gene expression under two conditions...

BINF 6203: Annotation with RAST

BINF 6203: Annotation with RAST

In this lab exercise, you’ll use the myRAST software (or the RAST website) to annotate an assembled genome. Try this first with the E. coli genome assembly that you generated a couple of weeks...

BINF 6203: NGS Genome Assembly

BINF 6203: NGS Genome Assembly

Part 1: assemble a chloroplast genome Today’s first challenge is to assemble the chloroplast genome data that was generated by the BINF 6350 class. You do not have to assemble all of the chloroplasts...