Non-Coding RNA (Jan 2022)

<i>DANSR</i>: A Tool for the Detection of Annotated and Novel Small RNAs

  • Jin Zhang,
  • Abdallah M. Eteleeb,
  • Emily B. Rozycki,
  • Matthew J. Inkman,
  • Amy Ly,
  • Russell E. Scharf,
  • Kay Jayachandran,
  • Bradley A. Krasnick,
  • Thomas Mazur,
  • Nicole M. White,
  • Ryan C. Fields,
  • Christopher A. Maher

DOI
https://doi.org/10.3390/ncrna8010009
Journal volume & issue
Vol. 8, no. 1
p. 9

Abstract

Read online

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

Keywords