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RNA-Seq Analysis Workshop
Welcome to the Trinity RNA-Seq analysis workshop! Here we will cover RNA-Seq analysis using genome-guided and/or genome-free methods:
For the genome-free methods, we'll be using Trinity (of course!), and cover de novo transcript assembly followed by transcript quantitation and differential expression analysis.
For the genome-guided RNA-Seq workshop, we'll use the highly popular Tuxedo toolkit.
An overview of these methodologies is presented in the accompanying workshop slides.
The workshop involves hands-on learning in applying the above computational methods to sample RNA-Seq data. The RNA-Seq data involve paired-end 76 base strand-specific Illumina RNA-Seq reads corresponding to Schizosaccharoymyces pombe (fission yeast) being grown under 4 different conditions: logarithmic growth (Sp_log), plateau phase (Sp_plat), heat shock (Sp_hs), and diauxic shift (Sp_ds). These data were generated as part of our previous publications ( Rhind et al. and Grabherr et al. ).
The raw data and all the software required to complete the workshop are built into a VirtualBox image as Trinity2015.ova. To install it, you'll first need VirtualBox installed - which is free and easy to do. Then simply follow the instructions to import and run the workshop VM.
The Trinity and Tuxedo workshops leverage the same input data, but are otherwise independent analysis trajectories. Simply choose which one you'd like to run through and begin: