2014 / December / mRNAseq on model organisms

This workshop was given on December 4th and 5th, 2014, by C. Titus Brown and Matt Scholz.

Tutorials:

• Short read quality and trimming
  • 0. Getting the data
  • 1. Copying in some data to work with.
  • 2. FastQC
  • 3. Trimmomatic
  • 4. FastQC again
• Mapping reads to the transcriptome with TopHat
  • Mapping reads
  • Counting mapped reads percentage
• Counting the reads that map to each gene
• Processing another sample with TopHat and HTSeq
• Data analysis & differential expression
  • Running edgeR on a data subset
  • Functional and network analysis on differentially expressed genes
• Submitting jobs to the MSU HPC queue
• Miscellaneous advice
  • Sequencing depth and number of samples
  • Downloading your data
  • Developing your own pipeline
• More resources
  • Informational resources
  • Places to share data, scripts, and results files

---

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

---