Data Wrangling and Processing for Transcriptomics: Key Points

Introduction and Experimental Planning Considerations for RNA-Seq

RNA-Seq is a powerful tool for understanding differences in gene expression in various experiments.
There are many ways to analyze these data, and we will show you one of them.
It is important to record and understand your experiment’s metadata.
Carefully plan your experiment to account for potential sources of variability.
Use appropriate numbers of biological replicates and consider technical replicates where necessary.
Randomize sample processing and use block designs to minimize bias.
Address batch effects during both the design and analysis stages.

Quality encodings vary across sequencing platforms.
for loops let you perform the same set of operations on multiple files with a single command.

Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.
To use most powerful bioinformatic tools, you will need to use the command line.
There are many different file formats for storing genomics data. It is important to understand what type of information is contained in each file, and how it was derived.