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RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

机译:RNASeqBrowser:一种基因组浏览器,用于同时可视化原始链特异的RNAseq读数和UCSC基因组浏览器自定义轨道

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摘要

BackgroundududStrand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets.ududResultsududThis paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform.ududConclusionsududThe features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously.ududRNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite
机译:背景 ud udRNA特定序列的RNAseq数据现在在RNAseq项目中更为常见。可视化RNAseq数据已成为测序数据分析中的重要内容。使用最广泛的可视化工具是UCSC基因组浏览器,该浏览器引入了自定义跟踪概念,使研究人员能够通过多个实验同时可视化特定位置的基因表达。该软件工具的目标是为RNAseq数据集的可视化提供友好的界面。 ud udResults ud ud本文介绍了一种可视化工具(RNASeqBrowser),该工具结合并扩展了UCSC基因组浏览器的功能。例如,RNASeqBrowser同时显示读取覆盖率,SNP,InDels和原始读取轨道以及其他BED和摆动轨道-所有这些都是从BAM文件动态生成的。配对的读段也连接在浏览器中,以使新的外显子/内含子边界和嵌合体转录物的鉴定更加容易。 RNASeqBrowser还支持链特异的RNAseq数据,该数据在中心线上方(正链转录物)或下方(负链转录物)显示读数。最终,RNASeqBrowser的设计目的是为那些缺乏生物信息学技能的用户提供易于使用的功能,并将许多基因组浏览器的功能整合到一个平台中。可视化工具,例如IGV。它通过添加几种新型轨道来显示NGS数据(例如单个原始读取,SNP和InDels)来扩展UCSC基因组浏览器的功能。 (2)RNASeqBrowser可以动态生成RNA二级结构。它对于识别非编码RNA(例如miRNA)很有用。 (3)覆盖NGS摆动数据有助于显示差异表达,并且在RNASeqBrowser中易于实现。 (4)NGS数据累积了大量原始读取。因此,RNASeqBrowser折叠精确的重复读取以减少可视化空间。普通PC可以显示许多NGS单个原始读取窗口,而不会出现太多延迟。 (5)单个原始读取的多个弹出窗口为用户提供了更大的查看空间。这避免了将所有原始读取都压缩到一个窗口中的现有方法(例如IGV)。这将有助于同时可视化多个数据集。 ud udRNASeqBrowser及其手册可从http://www.australianprostatecentre.org/research/software/rnaseqbrowser网站或http://sourceforge.net/projects/rnaseqbrowser/免费获得。网站

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