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Useful RNA-seq resources are summarized on our Resources tool list, Transcriptome analaysis section. The most important of these resources for Tuxedo are:
- the original RNAseq analysis protocol using Tuxedo article in Nature Protocols, and
- the URL for Tuxedo resource bundles for selected organisms (gff annotations, pre-built bowtie references, etc.)
Objectives
In this lab, you will explore a fairly typical RNA-seq analysis workflow using the Tuxedo pipeline. Simulated RNA-seq data will be provided to you; the data contains 75 bp paired-end reads that have been generated in silico to replicate real gene count data from Drosophila. The data simulates two biological groups with three biological replicates per group (6 samples total). This simulated data has already been run through a basic RNA-seq analysis workflow. We will look at:
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