Reference-Based Identification of Long Noncoding RNAs in Plants with Strand-Specific RNA-Sequencing Data.

Long noncoding RNAs (lncRNAs) have been shown to play important roles in various organisms, including plant species. Several tools and pipelines have emerged for lncRNA identification, including reference-based transcriptome assembly pipelines and various coding potential calculating tools. In this protocol, we have integrated some of the most updated computational tools and described the procedures step-by-step for identifying lncRNAs from plant strand-specific RNA-sequencing datasets. We will start from clean RNA-sequencing reads, followed by reference-based transcriptome assembly, filtering of known genes, and lncRNA prediction. At the end point, users will obtain a set of predicted lncRNAs for downstream use.