Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China.
School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, Jiangsu, China.
BMC Bioinformatics. 2018 Jul 13;19(1):260. doi: 10.1186/s12859-018-2266-3.
Methylated RNA immunoprecipitation sequencing (MeRIP-seq or mA-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic properties of RNA molecules and the intricate procedures of this technique, mA-seq data often suffer from various flaws. A convenient and comprehensive tool is needed to assess the quality of mA-seq data to ensure that they are suitable for subsequent analysis.
From a technical perspective, mA-seq can be considered as a combination of ChIP-seq and RNA-seq; hence, by effectively combing the data quality assessment metrics of the two techniques, we developed the trumpet R package for evaluation of mA-seq data quality. The trumpet package takes the aligned BAM files from mA-seq data together with the transcriptome information as the inputs to generate a quality assessment report in the HTML format.
The trumpet R package makes a valuable tool for assessing the data quality of mA-seq, and it is also applicable to other fragmented RNA immunoprecipitation sequencing techniques, including mA-seq, CeU-Seq, Ψ-seq, etc.
甲基化 RNA 免疫沉淀测序（MeRIP-seq 或 mA-seq）已被广泛用于分析 RNA N6-甲基腺苷修饰的转录组分布。然而，由于 RNA 分子的固有特性和该技术的复杂程序，mA-seq 数据通常存在各种缺陷。需要一种方便且全面的工具来评估 mA-seq 数据的质量，以确保它们适用于后续分析。
从技术角度来看，mA-seq 可以被视为 ChIP-seq 和 RNA-seq 的结合；因此，通过有效地结合这两种技术的数据质量评估指标，我们开发了 trumpet R 包来评估 mA-seq 数据的质量。trumpet 包将来自 mA-seq 数据的比对 BAM 文件与转录组信息一起作为输入，生成 HTML 格式的质量评估报告。
trumpet R 包是评估 mA-seq 数据质量的有价值工具，也适用于其他片段化 RNA 免疫沉淀测序技术，包括 mA-seq、CeU-Seq、Ψ-seq 等。
