This is the schedule for the 2015 MSU NGS course.
This workshop has a :doc:`code-of-conduct`.
Download all of these materials or visit the GitHub repository.
Meal Times: Breakfast 7-9, Lunch 12-1, Dinner 6-7 (Unless noted below)
This year we also ran a third week workshop focused on intermediate and advanced skills; please see the schedule at :doc:`week3`.
| Day | Schedule |
|---|---|
| Monday 8/10 |
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| Tuesday 8/11 |
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| Wed 8/12 |
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| Thursday 8/13 |
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| Friday 8/14 |
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| Saturday 8/15 |
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| Sunday 8/16 |
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| Monday 8/17 |
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| Tuesday 8/18 |
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| Wed 8/19 |
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| Thursday 8/20 |
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| Friday 8/21 |
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Instructors:
- C Titus Brown
- Chris Chandler
- Ian Dworkin
- Adina Howe
- Matt MacManes
- Meg Staton
TAs:
- Amanda Charbonneau
- Lisa Cohen
- Ryan Williams
- Phil Brooks
Lecturers:
- Nick Loman
- Torsten Seemann
- Erich Schwarz
She Who Drives Many Places:
- Jessica Mizzi
Practical Computing for Biologists
This is a highly recommended book for people looking for a systematic presentation on shell scripting, programming, UNIX, etc.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell et al., Nat. Protocols.
One paper that outlines a pipeline with the tophat, cufflinks, cuffdiffs and some associated R scripts.
Statistical design and analysis of RNA sequencing data., Auer and Doerge, Genetics, 2010.
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nookaew et al., Nucleic Acids Res. 2012.
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments Vijay et al., 2012.
Computational methods for transcriptome annotation and quantification using RNA-seq, Garber et al., Nat. Methods, 2011.
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments., Bullard et al., 2010.
A comparison of methods for differential expression analysis of RNA-seq data, Soneson and Delorenzi, BMC Bioinformatics, 2013.
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples., Wagner et al., Theory Biosci, 2012. Also see this blog post explaining the paper in detail.
- A Quick Guide to Organizing Computational Biology Projects, Noble, PLoS Comp Biology, 2009.
- Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results, Wicherts et al., PLoS One, 2011.
- Got replicability?, McCullough, Economics in Practice, 2007.
Also see this great pair of blog posts on organizing projects and research workflow.
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A high quality question & answer Web site.
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A discussion and information site for next-generation sequencing.
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A large number of open and reusable tutorials on the shell, programming, version control, etc.
http://www.genomesunzipped.org/
Genomes Unzipped.
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Titus's blog.
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Blue Collar Bioinformatics
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Mass Genomics
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Next Genetics
http://gettinggeneticsdone.blogspot.com/
Getting Genetics Done
http://omicsomics.blogspot.com/
Omics! Omics!
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Nick Loman's lab notebook
.. toctree:: :maxdepth: 5 day1 day2 variant assembling-ecoli-with-velvet interval-analysis-and-visualization sam-format-tutorial R_Introductory_tutorial_2014 IntroductionControlFlowR vcf_exploration eel-pond SOAPdeNovoTrans_count_eXpress analyzing_drosophila_htseq drosophila_rnaseq1 drosophila_rnaseq_bwa_htseq genome-comparison-and-phylogeny git-koans howe-mgrast howe-ncbi kmers-etc long-read mount_chris_snapshot short-read-quality-evaluation-ctb amazon/index instructors-guide code-of-conduct