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.
For full days, we anticipate a schedule something like this...
Tutorial/demo 1 (11am)
Tutorial/demo 2 (1:30pm)
Tutorial/demo 3 (7:30pm)
Arrive, check in, have dinner, hang out at the bonfire.
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)
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
Lecture: Thinking Statistically (Ian Dworkin)
Tutorial 1: Plotting with matplotlib
Entertainment: Brewery outing for dinner.
(No tutorial #3.)
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
Lecture: Assembly. (Titus Brown)
Tutorial 1: Short Read Assembly (Jason)
Tutorial 2: Visualizing NGS data on UCSC genome browser (Likit)
BBQ on Windmill Island.
Take a break - day of rest! Swim, sleep, make merry.
(Only lunch served.)
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)
Lecture: Resequencing analysis. (Jeff Barrick)
Tutorial, 11am: Storing data persistently with Amazon
Tutorial, 2:30pm: Writing Python scripts incrementally
Lecture, 8pm: ChIP-seq analysis. (Mark Robinson)
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!
(Half day: leave by noon.)
9am: Course post-mortem
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
Rose Canino-Koning, CS PhD student at MSU
Jason Pell, CS PhD student at MSU
Likit Preeyanon, MMG PhD student at MSU