Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data

Methods Mol Biol. 2022;2443:465-482. doi: 10.1007/978-1-0716-2067-0_24.

Abstract

Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length without discernible protein coding potential. Long intergenic noncoding RNAs (lincRNAs) constitute a subset of lncRNAs, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincRNA discovery from publicly available non-stranded RNA-Seq datasets. The pipeline presented can be applied to any plant species for which RNA-Seq data and a reference genome sequence are available.

Keywords: Genome annotation; Long intergenic noncoding RNA; RNA-Seq; Transcriptome; lincRNA.

MeSH terms

  • Genome
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / metabolism
  • RNA-Seq
  • Transcriptome

Substances

  • RNA, Long Noncoding