RNASeqSpring2012

= =

RNA-Seq Data Analysis Workshop

April 30, 2012
List of requirments:
 * __[|R]__ (version >= 2.14)
 * __[|Bioconductor]__ (version >= 2.9)

Reference
 * Oshlack //et al.// "From RNA-seq reads to differential expression results", //Genome Biology// 2010, **11**:220

1. [|Overview]

2. Read-mapping with or without a genome (Maurizio)
 * Possible mapping algorithms: [|bowtie], [|tophat], stampy
 * Material:
 * [|Overview] (docx)
 * [|CGRL_2012] (zip)

3. Normalization (Davide)
 * Material:
 * Normalization of RNA-Seq data [[|pdf]] [[|R code]]
 * Yeast RNA-Seq data from Risso et al. (2011) [__ [|R package] __] [[|tarball]]
 * Requirement:
 * __ [|EDASeq] __ package
 * Optional:
 * [|htseq] package

4. [|Statistics of RNA-seq differential expression testing] (OhKyu)

5. Differential expression testing using DESeq (Hana)

6. Downstream analysis: GO term/Gene Set Enrichment (Yulia)