Category: BINF 6203

BINF 6203: Genomics

BINF 6203: Genomics

This is the game plan for BINF 6203 — Genomics in Spring Semester 2015. Class times: 11:00-12:15 MW Lab: 12:15-2:00 M Links to these posts will also be provided in Moodle, but this post...

BINF 6203: Lab 8 — Simple variant calling

BINF 6203: Lab 8 — Simple variant calling

This lab takes us back to the tomato chloroplast genome data again. You’ve QCed the chloroplast data in Lab 2, assembled it in Lab 3, produced a consensus sequence from mapped reads in Lab...

BINF 6203: Lab 7 — Genome comparison with Mauve

BINF 6203: Lab 7 — Genome comparison with Mauve

As we started on comparative genomics, we covered three main concepts. First, how do you decide which genes are “the same” across multiple genomes, i.e. orthologs, genes having a common ancestor and related by...

BINF 6203: Lab 6 — Browsers and tracks

BINF 6203: Lab 6 — Browsers and tracks

You can think of genomic data formats in a few main categories: Sequence data (FASTA, FASTQ) Alignments (BLAST results, SAM and BAM files) Track data (genomic intervals, WIG files — continuous value tracks) Tabular data...

BINF 6203 — Lab 5: Generating annotation for a genome

BINF 6203 — Lab 5: Generating annotation for a genome

In this lab exercise, you’ll use the myRAST software to annotate an E. coli genome assembly that you generated a couple of weeks ago. We requested that myRAST be installed on the lab computers,...

BINF 6203 — Lab 4: Read mapping

BINF 6203 — Lab 4: 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...

Lab 3 part 2, my solution

Lab 3 part 2, my solution

Here’s how I approached the E. coli plus Pac Bio data at the command line. This problem was a little sneaky, so don’t worry if you didn’t figure out all of the aspects right...

BINF 6203: Lab 3 — Genome assembly

BINF 6203: Lab 3 — 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...

BINF 6203: Lab 2 — NGS Data QC

BINF 6203: Lab 2 — NGS Data QC

Today, you’ll use trimming software to clean up several NGS data sets. We’ll take a look at the following: Chloroplast genome sequences generated by Spring 2014 BINF 6350 students. (Ion Torrent, single end) Some...

BINF 6203: Lab 1 — Orientation

BINF 6203: Lab 1 — Orientation

The purpose of this lab exercise is to get you oriented to using genomic data sources, retrieving and converting files, loading files into CLC Genomics, etc. For this lab, you do not need to produce a...