Bioinformatic Analysis of Small RNA Sequencing Libraries

Methods Mol Biol. 2019:1932:51-63. doi: 10.1007/978-1-4939-9042-9_4.

Abstract

Bioinformatic analysis of small RNA sequencing libraries consists of transforming a series of small RNA sequencing experiment fastq files into a table containing small RNA sequences and their abundance. This is achieved by cleaning the reads, aligning the cleaned reads to a reference, and parsing the alignment results. In this protocol we present the most common option, and the rationale, for each of these steps.

Keywords: Adapter; Bioinformatics; Bowtie; Sequences; ShortStack; Small RNA; miRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • High-Throughput Nucleotide Sequencing / methods
  • MicroRNAs / genetics*
  • Sequence Analysis, RNA / methods
  • Software

Substances

  • MicroRNAs