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- Part 1: Tuxedo suite
- comparing tuxedo suite to other similar pipelines
- Part 2: RIP-Seq
- Theoretical and Experimental Background and Controls
- Protocol Variation and Primary Data Analysis
- Software Overview
- DESeq, edgeR
- Tuxedo (Cufflinks/Cuffdiff, Auxiliary tools)
- RipSeeker, ASPeak
- PARalyzer
- RIP-Seq Software
- Exercise #1: "Normal" Case Study #1: Whole-mRNA RIP-Seq
- Case Study #2Exercise#2: CLIP, -Seq
- Exercise#3: PAR-CLIP, and Others
Day 4: Downstream Analysis of Differentially Expressed Genes
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