Just as RNA itself has primary and secondary structure, RNA-Seq analysis has primary, Secondary and even tertiary steps. Which is the right tool at each step?
As a biologist, one of the most important things you should do before you start any experiment is to decide how you will handle and analyze the data that is generated. Whether done in bulk or with single cell resolution gene expression and regulation studies it now routinely generates large amount of data. In addition to the reads themselves there are also other tag sequences such as sample IDs, Cell IDs, UMIs and other meta-data about the samples. It is a good idea to think ahead and decide before you start which bioinformatic pipelines, base callers, aligners, statistical tests and even visualization tools you want to use.
There are multiple options at each of the steps of the workflow. Illumina has compiled a reference of many of the most popular analysis tools for each step in the process of turning raw data into biological insights. Click here to learn more about the different options available by downloading our e-Book “Critical Considerations for the Analysis of Gene Expression and Regulation Studies”