DIY.TRANSCRIPTOMICS

Learn all about Illumina's 'Sequencing by Synthesis' technology, and the steps involved in planning for a transcriptomics experiment... In this class we'll finally get down to the business of using Kallisto for memory-efficient mapping of your raw reads. You'll carry out this mapping in class, right on your laptop, while we discuss what's happening under the hood. During this process, we'll touch on a range of topics, from reference files, to command line basics, and using shell scripts for automation and reproducibility... Now that we've aligned our reads, it's time to discuss units for measuring gene expression. We'll discuss differences between RPKM and TPM, and how these units relate to basic properties of your reference file and data. We'll also discuss normalization within and between samples. To conclude this class, we'll fire up RStudio and take a look at our first script.