PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq

被引：27

作者：

Gao, Yubang ^{[1
]}

Wang, Huiyuan ^{[1
]}

Zhang, Hangxiao ^{[1
]}

Wang, Yongsheng ^{[1
]}

Chen, Jinfeng ^{[2
]}

Gu, Lianfeng ^{[1
]}

机构：

[1] Fujian Agr & Forestry Univ, Coll Life Sci, Fujian Prov Key Lab Haixia Appl Plant Syst Biol, Basic Forestry & Prote Res Ctr, Fuzhou 350002, Fujian, Peoples R China

[2] Univ Calif Riverside, Inst Integrat Genome Biol, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA

来源：

BIOINFORMATICS | 2018年 / 34卷 / 09期

基金：

中国国家自然科学基金;

关键词：

RNA; TRANSCRIPTOME; PACKAGE;

D O I：

10.1093/bioinformatics/btx830

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results.

引用

页码：1580 / 1582

页数：3

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