Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform
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Published on: May 16, 2020
Luis Augusto Eijy Nagai1, Seohyun Lee1, Ryuichiro Nakato1
1Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-0032, Japan.
Abstract:
Here, we present a protocol for the identification of differentially expressed genes through RNA sequencing analysis. Starting with FASTQ files from public datasets, this protocol leverages RumBall within a self-contained Docker system. We describe the steps for software setup, obtaining data, read mapping, sample normalization, statistical modeling, and gene ontology enrichment. We then detail procedures for interpreting results with plots and tables. RumBall internally utilizes popular tools, ensuring a comprehensive understanding of the analysis process.
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