Identification and Expression Analysis of Long Intergenic Noncoding RNAs

Methods Mol Biol. 2018:1751:139-152. doi: 10.1007/978-1-4939-7710-9_10.

Abstract

Long intergenic noncoding RNAs (lincRNAs) have caught increasing attention in recent years. The advance of RNA-Seq has greatly facilitated the discovery of novel lincRNAs. However, the computational analysis of lincRNAs is still challenging. In this protocol, we presented a step-by-step protocol for computational analyses of lincRNAs, including read processing and alignment, transcript assembly, lincRNA identification and annotation, and differential expression analysis.

Keywords: CPAT; Cufflinks; Differential expression; Noncoding RNA; RNA-Seq; STAR; lincRNA; lncRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Molecular Sequence Annotation
  • RNA, Long Noncoding / analysis*
  • RNA, Long Noncoding / genetics*

Substances

  • RNA, Long Noncoding