Abstract：
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We present splice_sim, a splice-aware RNA-seq simulation and evaluation pipeline that introduces user-defined nucleotide conversions at set frequencies, creates mixture models of converted and unconverted reads, and calculates mapping accuracies per genomic annotation. By simulating nucleotide conversion RNA-seq datasets under realistic experimental conditions, including metabolic RNA labeling and RNA bisulfite sequencing, we measure mapping accuracies of state-of-the-art spliced-read mappers for mouse and human transcripts and derive strategies to prevent biases in the data interpretation.
摘要：
核苷酸转换RNA测序技术询问细胞转录物中的化学RNA修饰，导致包含错配的读取。将所得读段映射到参考基因组的偏差仍然知之甚少。我们介绍splice_sim，剪接感知RNA-seq模拟和评估管道，以设定频率引入用户定义的核苷酸转换，创建转换和未转换读取的混合模型，并计算每个基因组注释的映射精度。通过在现实实验条件下模拟核苷酸转换RNA-seq数据集，包括代谢RNA标记和RNA亚硫酸氢盐测序，我们测量了小鼠和人类转录本的最先进的剪接阅读映射器的作图精度，并得出了防止数据解释偏差的策略。
