Monday

• Introduction
• Logging In and transferring files
• Intro to command-line
• Advanced command-line
• What is Bioinformatics? (talk)
• Running jobs on the Cluster and using modules

Tuesday

• Files and Filetypes for RNA-Seq (talk)
• Experimental Design and Cost Estimation (talk)
• Workshop dataset talk (Emily Rustad)
• Philosophy of Preprocessing Data (talk)
• Preprocessing Data hands-on

Wednesday

• Intro to Sequencing, Lutz Froenicke (talk)
• Aligners (talk)
• Contamination detection
• Tag-Seq vs. RNA-Seq (talk)
• Aligning Data and IGV

Thursday

• Intro to R
• Differential Gene Expression Statistics (talk)
• Alignments to Counts
• DE Analysis: counts to lists of DE genes
• Bacterial RNASeq (talk)

Friday

• Transript Assembly/Annotation (talk)
• GO/KEGG Pathway Enrichment: GO, KEGG
• Single Cell RNA-Seq (talk)
• Generating figures
• Closing thoughts

Evaluation!

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