Transcript Document

Oryza group
Arjan, Claire, Robert & Ruud
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
RNAseq data
Trimmed
Untrimmed
TopHat
Oryza group
TopHat
Use Samtools to check
coverage of mapped genome
(Considerable difference
between trimmed and
untrimmed sequences?)
Cufflinks
Oryza group
Cufflinks
Pick up the 100 most highly
expressed genes in the yeast
RNAseq (Robert)
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?