ANGUS

ANGUS, a number of detailedtutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis


(1) how to do basic scientific data analysis on UNIX

UNIX, ssh, and scp

Renting a computer from Amazon

Running BLASTs on UNIX

UNIX, BLAST, and long-running jobs

Working with CSV files and Python

Plotting with matplotlib

Scripts, Reciprocal Best-Hits BLAST, and some more Python

Mapping with bowtie

Visualizing mappings with Samtools

Other mappers

Short Read Assembly

Visualizing NGS data on UCSC genome browser

Simple mRNAseq: mapping reads to gene sets and doing quantile normalization

Gene differential expression using DEGseq

Analyzing bacterial resequencing data with breseq

Storing data persistently with Amazon

Writing Python scripts incrementally

Aligning ChIP-seq reads and detecting enriched peaks

Using MEME to identify TF binding motif from ChIP-seq data

Slightly more advanced scripting with Python

Using the Nano editor

Using ‘top’ to monitor running jobs

Setting a password rather than using your key

(2) Course Schedule (2010)

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

Bonfire!

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

Bonfire!

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

(3) tutorials of 2011
http://ged.msu.edu/angus/tutorials-2011/index.html