ProkSeq for complete analysis of RNA-Seq data from prokaryotes
Bioinformatics. 2020 Dec 26, Online ahead of print
Mahmud AKMF, Delhomme N, Nandi S, Fällman M

Abstract
Summary: Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, the current tools for studying gene expression, determination of differential gene expression, downstream pathway analysis, and normalization of data collected in extreme biological conditions is still lacking. Here we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data, and visualizing data and results.

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