scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator.
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scReadSim：单细胞RNA-seq和ATAC-seq读取模拟器。
DOI：
10.1038/s41467-023-43162-w
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发表时间：
2023-11-18
影响因子：
16.6
通讯作者：
Li, Jingyi Jessica
中科院分区：
文献类型：
--
作者：
Yan, Guanao;Song, Dongyuan;Li, Jingyi Jessica
使用测序（scATAC-seq）计算工具对单细胞RNA-seq （scRNA-seq）和转座酶可及染色质单细胞测定进行基准测试，需要模拟器来生成真实的测序读数。然而，这些为数不多的读取模拟器都无法模拟真实数据。为了填补这一空白，我们引入了scReadSim，这是一个单细胞RNA-seq和ATAC-seq读取模拟器，它允许用户指定基本事实，并通过模拟真实数据生成合成测序读取（在FASTQ或BAM文件中）。在读取序列和读取计数级别上，scReadSim模拟真实的scRNA-seq和scATAC-seq数据。此外，scReadSim提供了基础事实，包括scRNA-seq的唯一分子标识符（UMI）计数和scacac -seq的开放染色质区域。特别是，scReadSim允许用户设计细胞类型特异性的基真开放染色质区域，用于scATAC-seq数据生成。在scReadSim的基准测试应用中，我们发现UMI-tools在scRNA-seq的UMI重复数据删除中达到了最高的精度，而HMMRATAC和MACS3在scatta -seq的峰值调用中达到了最高的性能。分析单细胞测序数据的基准计算工具需要模拟真实的测序读数。然而，现有的几个读取模拟器中没有一个旨在模拟真实数据。在这里，作者介绍scReadSim，一个单细胞RNA-seq和ATAC-seq读取模拟器，通过模拟真实数据来工作。
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling. Benchmarking computational tools for analysis of single-cell sequencing data demands simulation of realistic sequencing reads. However, none of the few existing read simulators aim to mimic real data. Here, the authors introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that works by mimicking real data.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
影响因子：
9.8
作者：
Flati T;Gioiosa S;Chillemi G;Mele A;Oliverio A;Mannironi C;Rinaldi A;Castrignanò T
通讯作者：
Castrignanò T
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
从单细胞RNA-seq数据中提取信号的一般而灵活的方法。
影响因子：
16.6
作者：
Risso D;Perraudeau F;Gribkova S;Dudoit S;Vert JP
通讯作者：
Vert JP