Transcript Comparative transcriptomics of fungi

Comparative
transcriptomics
of fungi
Group Nicotiana
Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki
Research objective
To study differences in gene expression in
related fungi species
Studies species:
- Reference genome
- RNA reads > 100 bp
- Preferably: Paired-end
- Related species (or at least: single-celled,
eukaryotic)
- Similar conditions
Data Management
- Cleaning and trimming reads: FastQC (< 25)
Under Pipeline:
- Mapping reads: TopHat
- Assemble and quantify transcripts: Cufflinks
- Final transcriptome assembly: Cuffmerge
- Extracting the transcripts: gffread
Data Management
Correlation between expressed gene and transcript
properties
• determine GC content and transcript length
• determine intron length
• codon usage (loop analysis codon by codon;
count frequencies of codons in array )
Validation
• Run scripts on small, example datasets
automating in the pipeline
Data Processing
Module building
• Organize the components of our project
• Separate project in functional blocks
Visualization and Interaction network
• Compare different dataset or same species in
different conditions -- Cuffdiff
• R and Cytoscape to make visualization in
interaction network