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Next-Gen Sequence Analysis Workshop (2014)

This is the schedule for the 2014 MSU NGS course.

This workshop has a Workshop Code of Conduct.

Download all of these materials or visit the GitHub repository.

Day	Schedule
Monday 8/4	1:30pm lecture: Welcome! (Titus) Tutorial: Day 1 - Getting started with Amazon 7pm: research presentations
Tuesday 8/5	Day 2 – Running BLAST and other things at the command line 9:15am lecture: Sequencing considerations (Titus) 10:30am: tutorial, Running command-line BLAST (Titus) Afternoon: assessment 1:15pm: tutorial, Short Read Quality Control (Elijah and Istvan) (CTB alternate version Evaluating the quality of your short reads, and trimming them) Evening: firepit social
Wed 8/6	9:15am lecture: Mapping and Assembly (Titus) 10:30am: tutorial, Variant calling (Titus) 1:15pm: Understanding the SAM format (Istvan) 7:15pm: tutorial, UNIX command line (Elijah)
Thursday 8/7	9:15am lecture: Genomic Intervals (Istvan) 10:30am mini-diversion: The Bioinformatics Skill System (Istvan) 10:45am: tutorial, Interval Analysis and Visualization (Istvan) 1:15pm: tutorial, Assembling E. coli sequences with Velvet (Titus) 5:30pm: leave for Kalamazoo
Friday 8/8	9:15am-noon lecture/tutorial, R Tutorial for NGS2014 R etc. (Ian Dworkin and Martin Schilling) 1:15pm: tutorial, Variant calling and exploration of polymorphisms 1:15pm: lecture, more variant calling (Martin Schilling) 7pm: lecture, Gene and genome annotation: PowerPoint \| PDF (Daniel Standage)
Saturday 8/9	9:15am-noon: lecture/tutorial, A complete de novo assembly and annotation protocol for mRNASeq (Titus) 1:15pm: lecture/discussion, mRNAseq assembly with Trinity (Meg Staton)
Monday 8/11	9:15am lecture, mRNAseq and counting PDF (Ian Dworkin) 10:30am tutorial, RNA-seq: mapping to a reference genome with tophat and counting with HT-seq (Chris Chandler) 10:45am tutorial, RNASeq Transcript Mapping and Counting (BWA and HtSeq Flavor) (Meg) 2:15pm tutorial, Assembly with SOAPdenovo-Trans (Matt) 7:15pm tutorial, Mapping reads to transcriptomes (Trinity and SOAP) and counting.
Tuesday 8/12	9:15am lecture, mRNAseq and counting lecture 2 PDF (Ian Dworkin) 11:00am tutorial, Analyzing RNA-seq counts with DESeq 1:15pm tutorial, RNA-seq: mapping to a reference genome with BWA and counting with HTSeq (Meg) 2:00pm lecture, A tableside discussion on transcriptome assembly PDF (Matt).
Wed 8/13	9:15am-3pm lecture/tutorial, So you want to get some sequencing data in NCBI? (Adina) 7:15pm: Automation, scripts, git, and GitHub 8:15pm: firepit and a gin social
Thursday 8/14	9:15-10:15 lecture: Phylogeny-based methods for analysing genomes and metagenomes (Aaron Darling) 10:30am-noon tutorial: Genome comparison and phylogeny (Aaron) 1:15pm lecture / tutorial Looking at k-mer abundance distributions (Titus) 3pm long reads lecture / tutorial PacBio Tutorial (Matt MacManes) 6pm: BBQ (no dinner at McCrary) 8pm: invited speaker (NGS/EDAMAME) Jack Gilbert Note: Talk is in academic building auditorium. 9:15pm: firepit
Friday 8/15	9:15-9:45 closing lecture (Titus) 10am discussion about class; more stuff Links: Opinionated guides to NGS / Software Carpentry

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