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...
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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...
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)
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
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 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
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
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
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...