Warning
These documents are not maintained and their instructions may be out of date.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 |
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| Tuesday 6/11 |
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| Wednesday 6/12 |
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| Thursday 6/13 |
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| Friday 6/14 |
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| Saturday 6/15 |
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| Sunday 6/16 | Day of rest. Brunch in the morning; takeout dinner in evening. |
| Monday 6/17 |
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| Tuesday 6/18 |
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| Wednesday 6/19 |
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| Thursday 6/20 |
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| Friday 6/21 |
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- 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;
Instructors:
TAs:
Lecturers:
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.
Also see this great pair of blog posts on organizing projects and research workflow.
A high quality question & answer Web site.
A discussion and information site for next-generation sequencing.
A large number of open and reusable tutorials on the shell, programming, version control, etc.
http://www.genomesunzipped.org/
Genomes Unzipped.
Titus’s blog.
Blue Collar Bioinformatics
Mass Genomics
Next Genetics
http://gettinggeneticsdone.blogspot.com/
Getting Genetics Done
http://omicsomics.blogspot.com/
Omics! Omics!