RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection

J Comput Biol. 2022 Aug;29(8):857-866. doi: 10.1089/cmb.2021.0603. Epub 2022 Jul 1.


With the constant increase of large-scale genomic data projects, automated and high-throughput quality assessment becomes a crucial component of any analysis. Whereas small projects often have a more homogeneous design and a manageable structure allowing for a manual per-sample analysis of quality, large-scale studies tend to be much more heterogeneous and complex. Many quality metrics have been developed to assess the quality of an individual sample on the raw read level. Degradation effects are typically assessed based on the RNA integrity (RIN) score, or on postalignment data. In this study, we show that single commonly used quality criteria such as the RIN score alone are not sufficient to ensure RNA sample quality. We developed a new approach and provide an efficient tool that estimates RNA sample degradation by computing the 5'/3' bias based on all genes in an alignment-free manner. That enables degradation assessment right after data generation and not during the analysis procedure allowing for early intervention in the sample handling process. Our analysis shows that this strategy is fast, robust to annotation and differences in library size, and provides complementary quality information to RIN scores enabling the accurate identification of degraded samples.

Keywords: RNA-seq; alignment-free; degradation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genomics
  • RNA Stability*
  • RNA* / chemistry
  • RNA* / genetics
  • Sequence Analysis, RNA / methods


  • RNA