Insect RNASeq data analysis pipeline

Author of the article:LIU JinDing1, 2ZHANG Zan1HUANG ShuiQing2LI Fei1

Author's Workplace：1.Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing210095, China；2. College of Information Science and Technology，Nanjing Agricultural University，Nanjing210095，China

Key Words：highthroughput RNA sequencing, short sequence alignment, transcriptome reconstruction, gene function annotation, gene expression quantification, gene differential expression

Abstract：With the rapid development of highthroughput RNA sequencing (RNASeq) technology and the rapidly decreasing cost of this method, RNASeq is becoming an important tool for biological research, especially investigating gene function at the transcriptome level. RNASeq typically reads sequences rapidly with a certain percentage of sequence errors and bias producing a huge amount of data. RNASeq data analysis faces lots of challenges. Here, we describe different RNA sequencing platforms, raw data generation processes and data filtering and introduce short sequence alignment, transcriptome assembly, functional annotation and gene expression analysis. Finally, we briefly review the application of RNASeq in insects. The prospects of RNASeq techniques and their application are also discussed.