Chapter 2 Introduction

RNASequest, is a three-in-one RNAseq data analysis, data/app management, and publishing framework. It consists of a reproducible, configurable Expression Analysis (EA) module, multi-faceted result exploration in Quickomics v2.0, Bookdown report and Online slide deck, and a centralized data management system of apps and results generated by the workflow for future queries.

Expression Analysis (EA) is a Converter from a set of RNAseq analysis output to QuickOmics (http://quickomics.bxgenomics.com) for interactive visualization.

The EA pipeline contains four main scripts:

• EAinit

  This is the first step of the pipeline. It creates a directory storing files necessary for future steps.

  By default, the directory will be named based on the date of running the pipeline. For example, EA20220328_0 will be created since today is 2022-03-28. If the user runs EA again for the same dataset, the last digit will add up to avoid duplications: EA20220328_1

• EAqc

  This is the second step of the pipeline.

  It analyzes the covariates against the expression to determine if the expression is needed to be adjusted.

• EArun

  After running EAqc, the following EArun step will perform differential expression analysis based on defined groups.

  It also produces QuickOmics objects for webserver loading.

• EAreport

  The next step, EAreport, will generate a user-friendly bookdown report to visualize the EA pipeline results.

• EA2DA

  The last step, EA2DA, produces 6 data files that are required for the OmicsView project import.