Day 3 take aways

We looked at  the portions of the RNA-Seq analysis pipeline, that comes after mapping data:  gene/transcript quantification and finding differentially expressed genes when we are not interested in novel genes. We also looked at the tuxedo pipeline for when we are interested in finding genes and transcripts not already in our annotated transcriptome.

Open

PART A

 1. Gene counting/transcript counting/quantification/abundance

  2. Differential expression analysis

PART B

Use the new tuxedo pipeline to assemble transcripts representative of your samples and identify DEGs among them. The new tuxedo pipeline is an immense improvement over the last one in terms of speed. The pipeline unfortunately has many steps and most steps are sequential. The output of one step becomes the input of the next:

BACK TO COURSE OUTLINE