Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data.
Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data.
复制标题
DOI：
10.1261/rna.079505.122
复制
发表时间：
2023-08
期刊：
影响因子：
4.5
通讯作者：
Chanfreau, Guillaume F
中科院分区：
文献类型：
--
作者：
DeMario, Samuel;Xu, Kevin;He, Kevin;Chanfreau, Guillaume F
RT-PCR和北方印迹长期以来一直用于研究单个基因的RNA异构体的使用。长读序测序的最新进展已经产生了关于这些RNA同种型的使用和丰度的前所未有的信息。然而，由于高信息密度，长读段测序数据的可视化仍然具有挑战性。为了缓解这些问题，我们开发了NanoBlot，这是一种开源的R软件包，可以从长读序数据中生成北方印迹和RT-PCR样图像。NanoBlot需要对齐、位置排序和索引的BAM文件。绘图基于ggplot 2，并且易于定制。NanoBlot的优点包括用于设计探针以可视化同种型的稳健系统，包括基于特定区域的存在或不存在排除读取，表示具有连续长度变化的同种型的优雅解决方案，以及使用不同颜色在同一图中覆盖多个基因的能力。我们目前的纳米印迹的例子相比，实际的北方印迹数据。除了传统的凝胶样图像，NanoBlot软件包还可以输出其他可视化，如小提琴图和3′-RACE样图，专注于3′-末端异构体可视化。NanoBlot软件包的使用应该为可视化长读段RNA测序数据的一些挑战提供了一个简单的答案。
RT-PCR and northern blots have long been used to study RNA isoforms usage for single genes. Recent advancements in long-read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues, we have developed NanoBlot, an open-source R-package that generates northern blot and RT-PCR-like images from long-read sequencing data. NanoBlot requires aligned, positionally sorted and indexed BAM files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlot include a robust system for designing probes to visualize isoforms including excluding reads based on the presence or absence of a specified region, an elegant solution to representing isoforms with continuous variations in length, and the ability to overlay multiple genes in the same plot using different colors. We present examples of nanoblots compared to actual northern blot data. In addition to traditional gel-like images, the NanoBlot package can also output other visualizations such as violin plots and 3′-RACE-like plots focused on 3′-end isoforms visualization. The use of the NanoBlot package should provide a simple answer to some of the challenges of visualizing long-read RNA-sequencing data.