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Research article - Peer-reviewed, 2021

ProkSeq for complete analysis of RNA-Seq data from prokaryotes

Mahmud, A. K. M. Firoj; Delhomme, Nicolas; Nandi, Soumyadeep; Fallman, Maria


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, 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.

Published in

2021, Volume: 37, number: 1, pages: 126-128

    UKÄ Subject classification

    Bioinformatics and Systems Biology

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