In Silico Analysis of Micro-RNA Sequencing Data

Ernesto Aparicio-Puerta, Bastian Fromm, Michael Hackenberg, Marc K. Halushka

Research output: Chapter in Book/Report/Conference proceedingChapter


High-throughput sequencing for micro-RNAs (miRNAs) to obtain expression estimates is a central method of molecular biology. Surprisingly, there are a number of different approaches to converting sequencing output into micro-RNA counts. Each has their own strengths and biases that impact on the final data that can be obtained from a sequencing run. This chapter serves to make the reader aware of the trade-offs one must consider in analyzing small RNA sequencing data. It then compares two methods, miRge2.0 and the sRNAbench and the steps utilized to output data from their tools.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages21
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Alignment
  • Bowtie
  • Micro-RNA
  • MirGeneDB
  • Small RNA sequencing
  • isomiR
  • miRBase

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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