Next-Gen Sequence Analysis Workshop (2013)


These documents are not maintained and their instructions may be out of date. However the GED Lab does maintain the khmer protocols which may cover similar topics. See also the installation instructions for the current version of the khmer project.

This is the schedule for the 2013 MSU NGS course, which ran from June 10th to June 20th, 2013. If you’re interested in this course in 2014, please see the 2014 announcement.

Day Schedule
Monday 6/10
Tuesday 6/11
Wednesday 6/12
Thursday 6/13
Friday 6/14
Saturday 6/15
  • 9:15am: lecture, Pipelines and Automation (Titus)
  • 10:45am: tutorial: Shell scripts and pipelines.
  • 1:15pm: tutorial, R (text | code) (Josh)
  • Evening: BBQ/dinner.
Sunday 6/16 Day of rest. Brunch in the morning; takeout dinner in evening.
Monday 6/17
  1. Mapping to the transcriptome with BWA
  2. Mapping RNA-seq reads to the genome with tophat
  3. Differential Expression Analysis with CuffDiff and MISO
  4. De novo RNA-Seq Assembly
Tuesday 6/18
Wednesday 6/19
Thursday 6/20
Friday 6/21
  • 9:15am: meet at classroom with bags; final lecture.
  • 10am: course post-mortem/analysis
  • 11am: lunch at Frona’s Pantry (optional!)

Cheat sheet for starting up an EC2 instance

  • use Amazon Machine Instance “ami-c17ec8a8”;
  • m1.large or larger;
  • make sure you are in the US East zone (Virgina) – see upper right;
  • make sure the security group you use has SSH and HTTPS enabled for inbound;

Dramatis personae


  • Istvan Albert
  • C Titus Brown
  • Ian Dworkin


  • Amanda Charbonneau
  • Michael Crusoe
  • Tristan De Buysscher
  • Joshua Herr
  • Elijah Lowe
  • Likit Preeyanon


  • Nick Beckloff
  • Rayan Chaikhi
  • Chris Chandler
  • Adina Chuang Howe
  • Erich Schwarz

Papers and References


Computing and Data

Also see this great pair of blog posts on organizing projects and research workflow.

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