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:
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
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.
After running EAqc, the following EArun step will perform differential expression analysis based on defined groups.
It also produces QuickOmics objects for webserver loading.
The next step, EAreport, will generate a user-friendly bookdown report to visualize the EA pipeline results.
The last step, EA2DA, produces 6 data files that are required for the OmicsView project import.