Day 5 - Expression Analysis with RNA-seq

Processing mRNA sequencing data and testing for differential expression.

Topics

Working with high-throughput sequencing datasets

Quality control

Modern DNA and RNA alignment strategies

Estimating magnitude of gene expression
Normalization options
- e.g. quantile, tmm (trimmed mean of M-values)

Differential expression testing

Testing for differential expression
Statistical significance
Centering strategies

Additional Recommended Reading

Optional: Revisiting Global Gene Expression Analysis. Cell 151:476 (2012). doi:10.1016/j.cell.2012.10.012

Materials

Notes Exercises Solutions

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Logistics

Date 19 August 2016

Time 10 am to 12 pm (Instruction) / 1 pm to 2 pm (Intro to Exercises and Q&A) / 4 pm to 5 pm (Q&A)

Room Countway 403

Teaching Staff

Peter Kharchenko (Course Director)

Tiziana Sanavia (Teaching Assistant)