A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

被引：197

作者：

Hoffmann, Steve ^{[1
,2
,3
,4
]}

Otto, Christian ^{[1
,2
,3
,4
]}

Doose, Gero ^{[1
,2
,3
,4
]}

Tanzer, Andrea ^{[5
]}

Langenberger, David ^{[1
,2
,3
,4
]}

Christ, Sabina ^{[6
]}

Kunz, Manfred ^{[7
]}

Holdt, Lesca M. ^{[4
,8
]}

Teupser, Daniel ^{[4
,8
]}

Hackermueller, Joerg ^{[2
,3
,6
,9
]}

Stadler, Peter F. ^{[1
,2
,3
,4
,5
,10
,11
,12
]}

机构：

[1] Univ Leipzig, Jr Res Grp Transcriptome Bioinformat, Haertelstr 16-18, D-04109 Leipzig, Germany

[2] Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-04109 Leipzig, Germany

[3] Univ Leipzig, Bioinformat Grp, D-04109 Leipzig, Germany

[4] Univ Leipzig, LIFE Res Ctr Civilizat Dis, D-04109 Leipzig, Germany

[5] Univ Vienna, Dept Theoret Chem, Vienna, Austria

[6] Fraunhofer Inst Cell Therapy & Immunol IZI, RNom Grp, Leipzig, Germany

[7] Univ Leipzig, Dept Dermatol Venerol & Allergol, D-04109 Leipzig, Germany

[8] Univ Munich, Inst Lab Med, Munich, Germany

[9] UFZ Helmholtz Ctr Environm Res, Dept Prote, Young Investigators Grp Bioinformat & Transcript, Leipzig, Germany

[10] Max Planck Inst Math Sci, Leipzig, Germany

[11] Univ Copenhagen, Ctr Noncoding RNA Technol & Hlth, Frederiksberg, Denmark

[12] Santa Fe Inst, Santa Fe, NM 87501 USA

来源：

GENOME BIOLOGY | 2014年 / 15卷 / 02期

关键词：

JUNCTIONS; ALIGNMENT; TRANSCRIPTOME;

D O I：

10.1186/gb-2014-15-2-r34

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products.

引用

页数：11

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