Weiß Elena, Friedel Caroline C
Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich 80333, Germany.
Bioinform Adv. 2023 Jul 4;3(1):vbad085. doi: 10.1093/bioadv/vbad085. eCollection 2023.
To date, no methods are available for the targeted identification of genomic subregions with differences in sequencing read distributions between two conditions. Existing approaches either only determine absolute read number changes, require predefined subdivisions of input windows or average across multiple genes.
Here, we present RegCFinder, which automatically identifies subregions of input windows with differences in read density between two conditions. For this purpose, the problem is defined as an instance of the all maximum scoring subsequences problem, which can be solved in linear time. Subsequently, statistical significance and differential usage of identified subregions are determined with DEXSeq. RegCFinder allows flexible definition of input windows to target the analysis to any regions of interests, e.g. promoters, gene bodies, peak regions and more. Furthermore, any type of sequencing assay can be used as input; thus, RegCFinder lends itself to a wide range of applications. We illustrate the usefulness of RegCFinder on two applications, where we can both confirm previous results and identify interesting gene subgroups with distinctive changes in read distributions.
RegCFinder is implemented as a workflow for the workflow management system Watchdog and available at: https://github.com/watchdog-wms/watchdog-wms-workflows/.
Supplementary data are available at online.
迄今为止，尚无方法可用于靶向识别在两种条件下测序读数分布存在差异的基因组子区域。现有方法要么仅确定绝对读数变化，要么需要对输入窗口进行预定义细分，要么对多个基因求平均值。
在此，我们展示了RegCFinder，它可自动识别输入窗口中在两种条件下读数密度存在差异的子区域。为此，该问题被定义为所有最大得分子序列问题的一个实例，可在线性时间内求解。随后，使用DEXSeq确定已识别子区域的统计显著性和差异使用情况。RegCFinder允许灵活定义输入窗口，以便将分析靶向到任何感兴趣的区域，例如启动子、基因体、峰区域等。此外，任何类型的测序分析都可用作输入；因此，RegCFinder适用于广泛的应用。我们在两个应用中展示了RegCFinder的实用性，在这两个应用中我们既可以证实先前的结果，又可以识别出读数分布有明显变化的有趣基因亚组。
RegCFinder作为工作流管理系统Watchdog的一个工作流实现，可在以下网址获取：https://github.com/watchdog-wms/watchdog-wms-workflows/。
补充数据可在网上获取。
