Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.
Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.
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DOI：
10.1016/j.ymeth.2013.10.015
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发表时间：
2014-02
期刊：
影响因子：
4.8
通讯作者：
Kudla, Grzegorz
中科院分区：
文献类型：
--
作者：
Travis, Anthony J.;Moody, Jonathan;Helwak, Aleksandra;Tollervey, David;Kudla, Grzegorz
蛋白质和RNA-RNA双链体之间的关联在基因表达的转录后调节中是重要的。CLASH（杂交体的交联、连接和测序）技术通过将与蛋白质复合物相关的两个RNA分子物理连接成单个嵌合RNA分子来捕获RNA-RNA相互作用。这些事件是相对罕见的，并且需要相当大的努力来检测由CLASH实验产生的数百万个非嵌合cDNA读段中的少量嵌合序列。我们提出了“hyb”生物信息学管道，我们开发的高通量cDNA测序数据分析CLASH实验。虽然hyb主要设计用于AGO CLASH数据，但也可用于其他高通量测序数据集中嵌合读段的检测和注释。我们使用BLAST、BLAST+、BLAT、pBLAT和Bowtie 2读段比对程序在测试数据集中检查了嵌合体检测的灵敏度和特异性。我们使用Flexbar预处理和随后使用Bowtie 2读取映射的组合，在最短的时间内获得了最可靠的结果。“hyb”软件在GNU GPL（通用公共许可证）下分发，可以从https://github.com/gkudla/hyb下载。
Associations between proteins and RNA–RNA duplexes are important in post-transcriptional regulation of gene expression. The CLASH (Cross-linking, Ligation and Sequencing of Hybrids) technique captures RNA–RNA interactions by physically joining two RNA molecules associated with a protein complex into a single chimeric RNA molecule. These events are relatively rare and considerable effort is needed to detect a small number of chimeric sequences amongst millions of non-chimeric cDNA reads resulting from a CLASH experiment. We present the “hyb” bioinformatics pipeline, which we developed to analyse high-throughput cDNA sequencing data from CLASH experiments. Although primarily designed for use with AGO CLASH data, hyb can also be used for the detection and annotation of chimeric reads in other high-throughput sequencing datasets. We examined the sensitivity and specificity of chimera detection in a test dataset using the BLAST, BLAST+, BLAT, pBLAT and Bowtie2 read alignment programs. We obtained the most reliable results in the shortest time using a combination of preprocessing with Flexbar and subsequent read-mapping using Bowtie2. The “hyb” software is distributed under the GNU GPL (General Public License) and can be downloaded from https://github.com/gkudla/hyb.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
64.8
作者：
Gong, Chenguang;Maquat, Lynne E.
通讯作者：
Maquat, Lynne E.
影响因子：
64.5
作者：
Helwak A;Kudla G;Dudnakova T;Tollervey D
通讯作者：
Tollervey D