MiCM Intro to RNA-seq
0.1 Introduction
This webpage is still incomplete. If you see mistakes or missing material, feel free to contact me or make a pull request!
RNA sequencing has become a focal point of genomics research due to its combined ability to identify and quantify transcripts through a single assay. Now, RNA-seq has become a staple tool used by researchers to investigate biological mechanisms and disease onset. Many protocols are now available depending on the exact analysis or data being used.
Currently, we can either map RNA-seq reads to a reference genome or assemble the reads de novo to map them onto a transcriptome. Organisms with well-annotated genomes such as our own have the ability to simply map reads to an annotated transcriptome or attempt to identify new reads.
It is also possible to be interested in specific types of RNA (miRNA, mRNA, lncRNA etc.). Can be combined with other genomics assays or biochemical assays to explore other functions (RNA-protein, RNA structure, RNA-RNA).
Different experimental scenarios could exhibit different optimal methods for quantification, normalization and downstream analysis. They also require thorough quality control to ensure the reproducibility of the observed results.
This workshop aims to introduce experimental and computational biologists to the processing and analysis of RNA-seq data. We will look at the different steps and tools required and what considerations to make depending on your research question.
0.2 Acknowledgements
This e-book was developed using material from the following sources:
Galaxy
DESeq2 vignette
OSCA Book
Reinnier Padilla (PhD Candidate @ McGill University)