Course Schedule (2010)

The next-gen sequence analysis course runs June 1 - June 11, 2010, every day but Sunday. Here’s an outline of what we have planned for each day, and by whom.

Daily schedule (roughly):

For full days, we anticipate a schedule something like this...

Breakfast (7-8am).

Lecture (9am)

Tutorial/demo 1 (11am)

Lunch (12-1pm)

Tutorial/demo 2 (1:30pm)

Dinner (6pm)

Tutorial/demo 3 (7:30pm)

Day 0 (Mon, May 31) - Arrival

Arrive, check in, have dinner, hang out at the bonfire.

Day 1 (Tue, June 1)

Lecture: Introduction to the course (Titus Brown)

Tutorial 1: UNIX, ssh, and scp

Tutorial 2: Renting a computer from Amazon

An Exercise in Reflection (Stage 1)

Day 2 (Wed, June 2)

Lecture: Computational Basics (Titus Brown)

Tutorial 1: Running BLASTs on UNIX

Tutorial 2: UNIX, BLAST, and long-running jobs

Tutorial 3: Working with CSV files and Python

Day 3 (Th, June 3)

Lecture: Thinking Statistically (Ian Dworkin)

Tutorial 1: Plotting with matplotlib

Tutorial 2: Scripts, Reciprocal Best-Hits BLAST, and some more Python

Entertainment: Brewery outing for dinner.

(No tutorial #3.)

Day 4 (Fri, June 4)

Lecture: Mapping Reads to Known Genomes (Titus Brown)

Tutorial 1: Mapping with bowtie

Tutorial 2: Visualizing mappings with Samtools (Rose)

Tutorial 3: Other mappers and Bowtie parameters


Day 5 (Sat, June 5)

Lecture: Assembly. (Titus Brown)

Tutorial 1: Short Read Assembly (Jason)

Tutorial 2: Visualizing NGS data on UCSC genome browser (Likit)

BBQ on Windmill Island.

Day 6 (Sun, June 6)

Take a break - day of rest! Swim, sleep, make merry.

(Only lunch served.)

Day 7 (Mon, June 7)

Lecture: mRNAseq analysis. (Titus Brown)

Tutorial 1 (11:30am): Simple mRNAseq: mapping reads to gene sets and doing quantile normalization

Tutorial 2 (1:30pm): Gene differential expression using DEGseq (Likit)

Tutorial 3 (3:30pm): UNIX directories and files - a quick introduction

Evening lecture: Doing science on software engineering (Greg Wilson)

Day 8 (Tue, June 8

Lecture: Resequencing analysis. (Jeff Barrick)

Tutorials: Analyzing bacterial resequencing data with breseq


Day 9 (Wed, June 9)

Tutorial, 11am: Storing data persistently with Amazon

Tutorial, 2:30pm: Writing Python scripts incrementally

Lecture, 8pm: ChIP-seq analysis. (Mark Robinson)

Day 10 (Th, June 10)

Tutorial, 9am: Aligning ChIP-seq reads and detecting enriched peaks

Tutorial, 2pm: Using MEME to identify TF binding motif from ChIP-seq data

Tutorial, 1:30pm: more-advanced-python-scripting

An Exercise in Reflection (Stage 2)

Lecture, 7pm: Summing up. (Titus Brown)

Stick a fork in it: G&T party and bonfire!

Day 11 (Fri, June 11) - Departure

(Half day: leave by noon.)

Concluding day.

9am: Course post-mortem

11am: leave



C Titus Brown, course director

Greg Wilson, supporting online materials

Ian Dworkin, lecturer on statistics

Jeff Barrick, lecturer on resequencing

Mark Robinson, lecture on ChIP-seq

Cruise Director:

Rose Canino-Koning, CS PhD student at MSU

Teaching Assistants:

Jason Pell, CS PhD student at MSU

Likit Preeyanon, MMG PhD student at MSU

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