SOAPfuse: an Algorithm for Identifying Fusion Transcripts from Paired-end RNA-Seq Data

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2013 Feb 16

PMID 23409703

Citations 116

Authors

Wenlong Jia

Kunlong Qiu

Minghui He

Pengfei Song

Quan Zhou

Feng Zhou

Yuan Yu

Dandan Zhu

Michael L Nickerson

Shengqing Wan

Xiangke Liao

Xiaoqian Zhu

Shaoliang Peng

Yingrui Li

Jun Wang

Guangwu Guo

Affiliations

Soon will be listed here.

Abstract

We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data. SOAPfuse applies an improved partial exhaustion algorithm to construct a library of fusion junction sequences, which can be used to efficiently identify fusion events, and employs a series of filters to nominate high-confidence fusion transcripts. Compared with other released tools, SOAPfuse achieves higher detection efficiency and consumed less computing resources. We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at http://soap.genomics.org.cn/soapfuse.html.

Citing Articles

Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.

Dorney R, Reis-das-Merces L, Schmitz U Methods Mol Biol. 2024; 2883:231-255.

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A New Approach of Detecting Fusion Oncogenes by RNA Sequencing Exon Coverage Analysis.

Zakharova G, Suntsova M, Rabushko E, Mohammad T, Drobyshev A, Seryakov A Cancers (Basel). 2024; 16(22).

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Genomic and transcriptomic landscape of human gastrointestinal stromal tumors.

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Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.

Tan Y, Mohanty V, Liang S, Dou J, Ma J, Kim K J Bioinform Syst Biol. 2024; 6(2):74-81.

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Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability.

Gupta A, Avadhanula S, Bashyam M Oncogene. 2024; 43(32):2449-2462.

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