上回书说到,在建库时,单细胞测序通过barcode区分来源不同细胞的RNA序列,但是在同一个细胞中,同一基因可能会产生多次转录,而PCR步骤也会产生重复读取。为了区分reads是来源于生物扩增还是PCR扩增,scRNA-seq采用在PCR扩增前在cDNA序列上引入UMI标记,确定单个cDNA扩增过程中产生的拷贝数。因此scRNA-seq的数据处理有以下几...
Seurat 是一个用于单细胞 RNA 测序 (scRNA-seq) 分析的 R 包。在 Seurat 中,可以使用以下标准来筛选 UMI(Unique Molecular Identifiers): 1. UMI 数量:可以根据 UMI 的数量来筛选细胞。例如,可以过滤掉 UMI 数大于 2500 或小于 200 的细胞。 2. 线粒体基因占比:每个细胞中线粒体基因数目占比超过 5%时,...
pbmc scRNA-seq—质量控制 () [1]代码可用于自行计算该指标:/hbctraining/scRNA-seq/blob/master/lessons/ [2]Scrublet:/AllonKleinLab/scrublet
Here, we describe the application of UTR-Seq, as a strategy to uncover cis-regulatory signals of RNA stability during early zebrafish embryogenesis. The method combines massively parallel reporter assays (MPRA) with computational regression models. It surveys the effect of tens of thousands of ...
UMI-tools作为一款专为处理带有UMI标签的RNA-seq数据设计的工具,凭借其强大的功能和易用性,在生物信息学领域广受好评。UMI-tools 有非常详细的官方文档(网址:https://umi-tools.readthedocs.io/en/latest/),在里面可以找到详细的使用说明、参数解释和示例等,是学习和使用的首选资料。你也可以借助 Galaxy 生信云平台...
RNA sequencing (RNA-seq) captures the transcriptomic repertoire and quantifies the expression levels of genes. When performed on single cells (scRNA-seq), it is a powerful tool for characterizing cellular heterogeneity and understanding complex biological process...
Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create count matrices for downstream analysis. Whil
•功能较为单一:虽然在单细胞RNA-seq处理上表现出色,但对于其他类型的数据支持较少。 总结 处理UMI数据是提高测序数据质量的重要步骤。选择合适的工具取决于你的项目需求。如果你需要一个功能全面、适应性强的工具,UMI-tools是个不错的选择;如果你的项目涉及单细胞RNA测序数据,Drop-seq Tools和Je-Suite提供了更为...
https://divingintogeneticsandgenomics.rbind.io/post/understand-10x-scrnaseq-and-scatac-fastqs/ Analysing 10X Single Cell RNASeq Data 10x的技术问题: How does Cell Ranger correct barcode sequencing errors? What is a barcode whitelist? 1 2
Hi. Thanks for creating this tool. I'm trying to do an analysis from a pre-print on some scRNA-seq data and I think UMI Tools might be appropriate. Here is the paper: http://biorxiv.org/content/early/2017/02/02/104844 Basically, there is...