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Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow

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Plant Epigenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1456))

Abstract

Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result. The exact commands and pieces of code are provided and hopefully can be adapted and used by other researchers to facilitate the study of small RNA regulation.

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Author information

Authors and Affiliations

  1. Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4

    Slava Ilnytskyy

  2. Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada

    Andriy Bilichak

Authors
  1. Slava Ilnytskyy
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  2. Andriy Bilichak
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Corresponding author

Correspondence to Slava Ilnytskyy .

Editor information

Editors and Affiliations

  1. Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada

    Igor Kovalchuk

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Ilnytskyy, S., Bilichak, A. (2017). Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow. In: Kovalchuk, I. (eds) Plant Epigenetics. Methods in Molecular Biology, vol 1456. Humana Press, Boston, MA. https://doi.org/10.1007/978-1-4899-7708-3_16

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  • DOI: https://doi.org/10.1007/978-1-4899-7708-3_16

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  • Publisher Name: Humana Press, Boston, MA

  • Print ISBN: 978-1-4899-7706-9

  • Online ISBN: 978-1-4899-7708-3

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