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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