With the development of the new generation of biotechnology and bioinformatics, studies on the transcriptome of eukaryotes have detected a number of long non-coding RNAs (lncRNAs) and the lncRNAs may play key functional roles in gene expression and regulation. Currently, high-throughput RNA-Seq has become the main technique for lncRNA study and several bioinformatic methods have been used to process and analyze the sequencing data for exploring lncRNAs' information including sequence, structure, expression, function and so on. This paper represents a pipeline for the lncRNA prediction based on RNA-Seq, and the relevant bioinformatic methods are reviewed comprehensively. We also discussed several challenges and future works related to the lncRNA study.