Comparative transcriptomics

of fungi

Group NicotianaDaan 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