Next-Gen Sequence Analysis Workshop (2013)

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.
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 6/16Day 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!)
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