bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.
bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.
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bcSeq：一个 R 软件包，用于高通量 shRNA 和 CRISPR 筛选中的快速序列作图。
DOI：
10.1093/bioinformatics/bty402
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发表时间：
2018
期刊：
影响因子：
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通讯作者：
Owzar,Kouros
中科院分区：
文献类型：
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作者：
Lin,Jiaxing;Gresham,Jeremy;Wang,Tongrong;Kim,SoYoung;Alvarez,James;Damrauer,JeffreyS;Floyd,Scott;Granek,Joshua;Allen,Andrew;Chan,Cliburn;Xie,Jichun;Owzar,Kouros
CRISPR-Cas9和shRNA高通量测序筛选在基础和转化研究中有着丰富的应用。用于分析这些筛选的方法和工具必须适当地考虑测序错误，以统计学原则的方式解决条形码文库中相似序列之间的模糊映射，并且在计算上是有效的。在这里，我们介绍了bcSeq，一个开源的R包，它实现了一个快速和并行化的算法，用于将高通量测序读数映射到条形码库，同时容忍测序错误。该算法使用Trie数据结构来提高速度，并通过使用基于每次读取的Phred分数的统计测序错误模型来解决模糊映射。可用性和实施该软件包的源代码和随附的教程可在http://bioconductor.org/packages/bcSeq/.Supplementary信息中获得补充数据可在Bioinformaticsonline获得。
SummaryCRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we presentbcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read.Availability and implementationThe package source code and an accompanying tutorial are available at http://bioconductor.org/packages/bcSeq/.Supplementary informationSupplementary data are available atBioinformaticsonline.