**5. Concluding remarks**

In the past few years, recent advances in sequencing technologies allowed the cost‐efficient generation of an unprecedented amount of biological information. Similarly, RNA‐seq tech‐ niques are under continuous improvements allowing wide range applications and develop‐ ment of high level resolution experiments such as those based on the emergent single‐cell RNA sequencing (scRNA‐seq) field. To couple with this ever increasing data, several tools and pipelines have been constantly developed. The bioinformatics field changes in an astonishing pace, in a way that it is almost impossible to keep up with all the new tenden‐ cies, the overwhelming amount of available software and the controversial opinions in the scientific community. For some aspects, it is difficult to find a consensus on the best pipeline to be applied. This chapter goal was to guide RNA‐seq users through its complex steps, providing a brief overview of the complete workflow, highlighting accessible protocols and currently available tools, most of which correlated with supporting benchmark studies.
