TopHat: discovering splice junctions with RNA-Seq.
TopHat: discovering splice junctions with RNA-Seq.
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DOI：
10.1093/bioinformatics/btp120
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发表时间：
2009-05-01
期刊：
影响因子：
--
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Trapnell C;Pachter L;Salzberg SL
动机：一种用于在称为RNA-seq的细胞中测序Messenger RNA的新协议，可以在单个运行中产生数百万个短序列片段，或者可以使用“读取”。确定基因的新型剪接变体，将RNA-Seq数据排列到基因组的当前软件依赖于已知的剪接连接，并且无法识别新颖的读数。旨在将RNA-Seq实验读取到参考基因组而不依赖已知的剪接位点。
结果：我们从最近的哺乳动物RNA-seq实验中绘制了RNA-Seq读取，并从该研究中恢复了基于注释的软件报告的72％以上的剪接连接，以及近20000个以前未报告的连接比以前的系统要快得多，绘制了近220万个CPU小时读取的速度，这足以在不到一天的时间内处理整个RNA-Seq实验标准桌面计算机。
可用性：Tophat是免费的，开源软件，可从http://tophat.cbcb.umd.edu获得
联系人：cole@cs.umd.edu
补充信息：可以在线生物信息学上获得补充数据。
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: cole@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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