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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

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Comparative transcriptomics of fungi

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  1. Comparative transcriptomicsof fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki

  2. 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

  3. 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

  4. 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

  5. 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

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