1. Martijn Masoed Nick Rico
Martijn
Masoed
Nick
Rico

2. Index
Dataset
TopHat, Cufflinks (1)
Cuffmerge, Cuffdiff, analyse (2)

3. Dataset Arabidopsis thaliana (advanced) Six conditions: Cold stress
Drought stress
Heat stress
Highlight stress
Salt stress
Control

4. Pipeline (1) Input data (FastQ) Tophat Bamfile Cufflinks
Transcripts.gtf

5. Biological interpretation
Pipeline (2)
Control vs condition
transcript.gtf
Cuffmerge
Merged.gtf
Bamfile
Cuffdiff
DE-genes
Get_functions
Biological interpretation

6. Time schedule Day 1 2 3 4 5 Task Make a planning.
Run tophat + cufflinks
Run cuffmerge + cuffdiff
Bio interpretation + GO analysis.
Planning presentation
Moduel of co-expressed genes. Advanced tasks
Check R (WGCMA)
Evt. Conserved modules.
Day 6 7 8 9 10
Task
Report
Wrap up project tasks
Wrap up project tasks
Report + presentation
Report + Presentation
Presentation

7. Questions