Instructor Notes

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1. Introduction to RNA-seqWhere are we heading towards in this workshop?

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2. Downloading and organizing files

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3. Quality control of RNA-seq reads

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4A. Genome-based quantification (STAR + featureCounts)

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4B. Transcript-based quantification (Kallisto)

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5A. Gene-level QC and differential expression (DESeq2)

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5B. Differential expression using DESeq2 (Kallisto pathway)

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6. Gene set enrichment analysis

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