Laura Saba, PhD
Department of Pharmaceutical Sciences
Skaggs School of Pharmacy and Pharmaceutical Scienes
Survey of best practices - Conesa et al 2016
Introduction to RNA-Seq - Kukurba and Montgomery 2015
Overview of RNA-Seq - Pepke et al 2009
RNA Separation - Mattick & Makunin 2006
RNA Separation - Genomes 2002
RNA Separation - Kukurba and Montgomery 2015
Library Preparation - Corney and Basturea 2013
Link to Illumina Video - Illumina Sequencing by Synthesis
Sequencing Depth - Sims et al 2014
ERCC Synthetic Spike-Ins - ThermoFisher
Popular Pipelines
- CuffLinks Protocol (older Tuxedo Pipeline) - Trapnell et al 2012
- StringTie Protocol (newer Tuxedo Pipeline) - Pertea et al 2016
- cutadapt
- Quality-based Trimming Recommendations - Williams et al 2016
- StringTie
- GTF File Format
- For visualization - UCSC Genome Browser
Alternative splicing - MISO
Alternative polyadenylation - DaPars
Influence of RNA extraction - Sultan et al 2014
RNA-Seq Power Analyses/Sample Size Calculations - Ching et al 2014
RNA-Seq Power Analyses/Sample Size Calculations - Bi and Lui 2016
RNA-Seq Power Analyses/Sample Size Calculations - Busby et al 2013
ERCC Synthetic Spike-Ins for RNA-Seq - Jiang et al 2011