TopHat: discovering splice junctions with RNA-Seq

Bioinformatics - Tập 25 Số 9 - Trang 1105-1111 - 2009
Cole Trapnell1, Lior Pachter1, Steven L. Salzberg1
11 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742 and 2Department of Mathematics, University of California, Berkeley, CA 94720, USA

Tóm tắt

Abstract Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu Contact:  [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.

Từ khóa


Tài liệu tham khảo

Abouelhoda, 2004, Replacing suffix trees with enhanced suffix arrays, J. Discrete Alg., 2, 53, 10.1016/S1570-8667(03)00065-0

Adams, 1993, Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library, Nat. Genet., 4, 373, 10.1038/ng0893-373

Burrows, 1994, A block sorting lossless data compression algorithm, Technical Report 124.

Cloonan, 2008, Stem cell transcriptome profiling via massive-scale mRNA sequencing, Nat. Meth., 5, 613, 10.1038/nmeth.1223

De Bona, 2008, Optimal spliced alignments of short sequence reads, Bioinformatics, 24, i174, 10.1093/bioinformatics/btn300

Döring, 2008, Seqan an efficient, generic c++library for sequence analysis, BMC Bioinformatics, 9, 11, 10.1186/1471-2105-9-11

Ferragina, 2001, An experimental study of an opportunistic index, Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms., 269

Hillier, 2008, Whole-genome sequencing and variant discovery in C. elegans, Nat. Meth., 5, 183, 10.1038/nmeth.1179

Kent, 2002, Blat—the blast-like alignment tool, Genome Res., 12, 656

Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25

Le Texier, 2006, Alttrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation, BMC Bioinformatics, 7, 169, 10.1186/1471-2105-7-169

Li, 2008, Mapping short dna sequencing reads and calling variants using mapping quality scores, Genome Res., 18, 1851, 10.1101/gr.078212.108

Marioni, 2008, RNA-Seq: an assessment of technical reproducibility and comparison with gene expression arrays, Genome Res., 18, 1509, 10.1101/gr.079558.108

Morinaga, 1996, Isolation of a brefeldin A-inhibited guanine nucleotide-exchange protein for ADP ribosylation factor (ARF) 1 and ARF3 that contains a Sec7-like domain, Proc. Natl Acad. Sci. USA, 93, 12856, 10.1073/pnas.93.23.12856

Mortazavi, 2008, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Meth., 5, 621, 10.1038/nmeth.1226

Pozzoli, 2007, Intron size in mammals: complexity comes to terms with economy, Trends Genet., 23, 20, 10.1016/j.tig.2006.10.003

Sultan, 2008, A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome, Science, 321, 956, 10.1126/science.1160342

Wang, 2008, Alternative isoform regulation in human tissue transcriptomes, Nature, 456, 470, 10.1038/nature07509

Wu, 2005, GMAP: a genomic mapping and alignment program for mRNA and EST sequences, Bioinformatics, 21, 1859, 10.1093/bioinformatics/bti310

Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res., 18, 821, 10.1101/gr.074492.107

Thông tin
Thông tin xuất bản

Bioinformatics

Tập 25 Số 9

1105-1111

Thông tin tác giả