This is the schedule for the 2014 MSU NGS course.
This workshop has a Workshop Code of Conduct.
Day | Schedule |
---|---|
Monday 8/4 |
|
Tuesday 8/5 |
|
Wednesday 8/6 |
|
Thursday 8/7 |
|
Friday 8/8 |
|
Saturday 8/9 |
|
Monday 8/11 |
|
Tuesday 8/12 |
|
Wednesday 8/13 |
|
Instructors:
TAs:
Lecturers:
He Who Drives Many Places:
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!