piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
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DOI：
10.1093/bioinformatics/btu647
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发表时间：
2015-02-15
期刊：
影响因子：
--
通讯作者：
Weng Z
中科院分区：
文献类型：
--
作者：
Han BW;Wang W;Zamore PD;Weng Z
动机：PIWI相互作用RNA（piRNA）是一种23-36 nt的小沉默RNA，可抑制后生动物种系中的转座子表达，从而保护基因组。尽管高通量测序使得以前所未有的分辨率检查基因组和转录组成为可能，但从千兆字节的测序数据中提取有用的信息仍然需要大量的计算技能。此外，研究人员可能会以不同的方式分析和解释相同的数据，产生难以协调的结果。为了解决这些问题，我们开发了一套协调的管道，“piPipes”，以分析来自各种高通量测序文库的皮尔纳和转座子衍生的RNA，包括小RNA、RNA、降解组或7-甲基鸟苷帽基因表达分析（CAGE）、染色质免疫沉淀（ChIP）和基因组DNA-seq。piPipes还可以生成适合发布的图形和表格。通过促进数据分析，piPipes为皮尔纳领域的计算方法标准化提供了机会。补充资料：补充信息，包括流程图和每个管道的示例图，可在生物信息学在线。可用性和实现：piPipes在Bash，C++，Python，Perl和R中实现。piPipes是免费的开源软件，在GPL v3许可证下分发，可在http://bowhan.github.io/piPipes/上获得。联系人：菲利普.扎莫尔@ umassmed.edu或Zhiping.Weng@ umassmed.edu补充信息：补充数据可在生物信息学在线获得。
Motivation: PIWI-interacting RNAs (piRNAs), 23–36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, ‘piPipes’, to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field. Supplementary information: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online. Availability and implementation: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http://bowhan.github.io/piPipes/. Contact: Phillip.Zamore@umassmed.edu or Zhiping.Weng@umassmed.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
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DOI：
10.1093/bioinformatics/btq216
发表时间：
2010-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hormozdiari F;Hajirasouliha I;Dao P;Hach F;Yorukoglu D;Alkan C;Eichler EE;Sahinalp SC
通讯作者：
Sahinalp SC
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影响因子：
3
作者：
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通讯作者：
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影响因子：
64.8
作者：
Reuter, Michael;Berninger, Philipp;Pillai, Ramesh S.
通讯作者：
Pillai, Ramesh S.