1. Case study: Saccharomyces cerevisiae grown under two different conditions RNAseq data plataform: Illumina Goal: Generate a platform where the user will input files and directory names, make the choice for trimmed or untrimmed RNAseq data to be assembled, and retrieve the top 100 expressed genes provided with biological information. Bioinformatics tools aimed to be used: TopHat, samtools, cufflinks, perl scripts, cytoscape (?) Oryza group Arjan, Claire, Robert & Ruud

2. RNAseq data Trimmed Oryza group Untrimmed TopHat

3. Oryza group TopHat Use Samtools to check coverage of mapped genome (Considerable difference between trimmed and untrimmed sequences?) Cufflinks

4. Oryza group Pick up the 100 most highly expressed genes in the yeast RNAseq (Robert) Cufflinks Biological questions on the selected genes: Correlation between exon/intron size and gene expression (Ruud); Develop a package to retrieve genes sequences (Arjan); Correlation between GC content and gene expression (Claire)... compare results with profile of less expressed genes?... compare differently expressed genes on both growth conditions?... GO annotation? Plot data on cytoscape?