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Practical Guide to Interpreting RNA-seq Data

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Practical Guide to Interpreting RNA-seq DataSkyler Kuhn1,2Mayank Tandon1,21. CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI2. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer ResearchOverviewI. Experimental DesignHypothesis-drivenOverview of Best PracticeII. Quality-controlPre- and post- alignment QC metricsInterpretationIII. PipelineFastQ Files -> Counts matrixReproducibility 1IV. Downstream AnalysisPrincipal Components Analysis (PCA)Differential ExpressionPathway AnalysisV. Advanced VisualizationsGroup comparisonsAlternative Splicing EventsPathway Diagrams Design: Overview Hypothesis-drivenAddresses a well thought-out quantifiable questionConsiderations: Library Construction: mRNA versus total RNASingle-end versus Paired-end SequencingSequencing Depth: quantifying gene-level or transcript-level expressionNumber of Replicates: statistical-power and ability

Practical Guide to Interpreting RNA-seq Data Skyler Kuhn1,2 Mayank Tandon1,2 1. CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI 2. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research

  Data, Interpreting

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