RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.
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DOI：
10.12688/f1000research.8964.1
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Barbry P
中科院分区：
文献类型：
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作者：
Popa A;Lebrigand K;Paquet A;Nottet N;Robbe-Sermesant K;Waldmann R;Barbry P
核糖体分析技术（Ribo-seq）允许对翻译RNA区域进行选择性测序。近年来，与Ribo-seq reads相关的基因组序列分析已被广泛用于评估其编码潜力。这些分析导致了在不同实验条件下差异翻译转录本的鉴定，和/或核糖体暂停在密码子基序上。在对分析核糖序列读取的工具的需求不断增长的背景下，我们开发了“核糖剖析”，一个新的Bioconductor开源软件包。“RiboProfiling”提供了一个完整的管道，涵盖核糖体足迹分析的所有关键步骤。这个管道已经在一个R工作流中实现了。该软件包将比对（BAM）文件作为输入，并在转录本水平上执行核糖体足迹量化。它还可以识别特定氨基酸或多氨基酸基序上的足迹积累。报表汇总图形和数据量化自动生成。该包有助于Ribo-seq实验的质量评估和定量。它在Bioconductor中的实现使其能够通过r中可用的大量软件包对其输出进行建模和统计分析。本文说明了如何根据大肠杆菌的数据识别积累核糖体足迹的密码子基序。
The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially translated transcripts under different experimental conditions, and/or ribosome pausing on codon motifs. In the context of the ever-growing need for tools analyzing Ribo-seq reads, we have developed ‘RiboProfiling’, a new Bioconductor open-source package. ‘RiboProfiling’ provides a full pipeline to cover all key steps for the analysis of ribosome footprints. This pipeline has been implemented in a single R workflow. The package takes an alignment (BAM) file as input and performs ribosome footprint quantification at a transcript level. It also identifies footprint accumulation on particular amino acids or multi amino-acids motifs. Report summary graphs and data quantification are generated automatically. The package facilitates quality assessment and quantification of Ribo-seq experiments. Its implementation in Bioconductor enables the modeling and statistical analysis of its output through the vast choice of packages available in R. This article illustrates how to identify codon-motifs accumulating ribosome footprints, based on data from Escherichia coli.