These documents are not maintained and their instructions may be out of date.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.
|Sunday 6/16||Day of rest. Brunch in the morning; takeout dinner in evening.|
- 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;
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.
Computational methods for transcriptome annotation and quantification using RNA-seq, Garber et al., Nat. Methods, 2011.
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.