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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...

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...