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.

Day	Schedule
Monday 6/10	1:30pm tutorial: Day 1 - Getting started with Amazon (Adina) 7pm: research presentations
Tuesday 6/11	Day 2 – Running BLAST and other things at the command line 9:30am: lecture, Welcome! (Titus) 10:45am: tutorial, Running command-line BLAST 1:15pm: tutorial, Evaluating the quality of your short reads, and trimming them Evening: firepit social
Wednesday 6/12	Day 3 – Mapping 9:30am: lecture, Mapping. (Titus) 10:45am: tutorial, Mapping reads with bwa and bowtie (Likit) 1:15pm: tutorial cont’d; also, Plotting the distribution of mapping mismatches 8pm: General bioinformatics overview (Istvan)
Thursday 6/13	9:15am: lecture, Assembly. (Titus) 10:45am: tutorial, Assembling E. coli sequences with Velvet 1:15pm: tutorial, cont’d, evaluating assemblies. Evening: brew pub in Kalamazoo.
Friday 6/14	9:15am: lecture, Intervals (Istvan) 10:45am: tutorial, Interval Analysis Tutorial (Istvan) 1:15pm: lecture/tutorial, Statistics (Ian) 8 Tutorial: Teach me interval based analysis (Istvan)
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	9:15am: lecture, mRNAseq I (Ian Dworkin) Tutorials 10:45am, 1:15pm as usual; topics: Mapping to the transcriptome with BWA Mapping RNA-seq reads to the genome with tophat Differential Expression Analysis with CuffDiff and MISO De novo RNA-Seq Assembly 7:30pm: Some git koans (Titus) 8-9pm: look busy 9pm: firepit
Tuesday 6/18	9:15am: lecture, mRNAseq II (Ian Dworkin) Impromptu tutorial: Using seqtk to trim and process reads at an insanely high speed Tutorials 10:45am, 1:15pm as usual; mRNAseq, continued. Counting reads for RNA-seq (edgeR code) 8:30pm: Single-cell mRNAseq (Erich Schwarz) 9:15pm: PacBio intro (Tristan De Buysscher) 8-11pm: look busy
Wednesday 6/19	9:15am: Advanced assembly (Rayan) 10:45am: Calculating k-mer abundance distributions and presentation (Titus) 1:15pm: Computing without Amazon (Michael Crusoe) 2pm: Calling SNPs with Samtools (Likit) 3-5pm: look busy. 7:30pm: BBQ, gin, and firepit social
Thursday 6/20	9:15am: lecture, Genome assembly and analysis (Erich Schwarz) 10:45am: Genome assembly treasure hunt. 1:15pm: Visualising Read Alignments on UCSC Genome (Likit) 5pm: Joe Graves, Genome-Wide Convergence with Repeated Evolution in Drosophila melanogaster. 8:30pm: Sequencing technology Q&A (Nick Beckloff) 8-11pm: look busy
Friday 6/21	9:15am: meet at classroom with bags; final lecture. 10am: course post-mortem/analysis 11am: lunch at Frona’s Pantry (optional!) Read more

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