Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
Highlights
We developed a proof-of-concept, well-documented “tutorial pipeline” over the course of a three-day NCBI-sponsored hackathon intended to teach RNA-seq and ChIP-seq analysis to beginners. This tutorial pipeline, “SeqAcademy,” incorporates state-of-the-art RNA sequencing (RNA-Seq) and ChIP-seq analysis tools into a simple, easy to use workflow tutorial and we demonstrate its use with publicly available data
The tutorial splits into two separate protocols: one for RNA-seq, the other for ChIP-seq analysis
We focused on using RNA-seq on “bulk” or homogenate tissue samples, as opposed to single-cell RNA-seq, which has distinct analytical considerations
Summary
Author roles: Ather SH: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Awe OI: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Writing – Original Draft Preparation, Writing – Review & Editing; Butler TJ: Conceptualization, Data Curation, Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing; Denka T: Conceptualization, Data Curation, Resources, Writing – Original Draft Preparation, Writing – Review & Editing; Semick SA: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Tang W: Data Curation, Formal Analysis, Methodology, Project Administration, Resources, Software, Writing – Review & Editing; Busby B: Conceptualization, Project Administration, Resources, Writing – Review & Editing
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