CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 20; pp. 3289 - 3291
• Main Authors: Wan, Changlin, Gao, Jianing, Zhang, Huan, Jiang, Xiaohua, Zang, Qiguang, Ban, Rongjun, Zhang, Yuanwei, Shi, Qinghua
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.10.2017
• Subjects: Animals; Applications Notes; Computational Biology - methods; Eukaryota - genetics; Eukaryota - metabolism; Gene Expression Regulation; High-Throughput Nucleotide Sequencing - methods; Humans; RNA, Untranslated - genetics; Sequence Analysis, RNA - methods; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btx066

Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research. CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/. zyuanwei@ustc.edu.cn or qshi@ustc.edu.cn. Supplementary data are available at Bioinformatics online.