CellRanger ARC 是10x Genomics 专为单细胞多组学数据分析设计,同时分析单细胞RNA测序(scRNA-seq)和单细胞ATAC测序(scATAC-seq)数据的一组分析pipline 。 主要包含以下几个方面: 数据预处理 将原始的测序数据转换为可分析的数据格式。 包括对FASTQ文件的读取、质量控制、去重复和对齐等步骤。 细胞检测和定量 自动检...
Cell Ranger 支持单细胞转录组(scRNA-seq)和免疫组库(TCR/BCR)等多种分析,广泛应用于生命科学研究中,是单细胞测序数据分析的核心工具。 关于cellranger的定量流程,前面已经多次分享了。参考: cellranger的定量流程合辑 非模式生物构建10x单细胞转录组CellRanger参考文件 CellRanger ARC—单细胞RNAseq和ATAC联合分析套件...
cellranger-arc需要多组学数据,也就是同一批次的样本,一部分用于单细胞转录组建库,一部分用于单细胞ATAC建库。 cellranger-arc mkfastq 从原始bcl文件生成fastq文件: cellranger-arc mkfastq--id=tiny-bcl-atac \--run=/home/yanyt/02.data/10.cellranger_arc_test/01.example_data/01.database/cellranger-arc...
1. 使用 '#require(magrittr)require(readr)require(Matrix)require(tidyr)require(dplyr)#---# # The path to dictopnary store the outpot of Cellrnager arc/ATAC mex_dir_path<-"/home/zhiyong/Desktop/AAAAAAA-LHJ-CXY-scRNA-ATAC---STAR/WT/snATAC/filtered_peak_bc_matrix"mtx_path<-paste(mex...
cellrangerarc/count/main.nf and cellrangerarc/mkref/main.nf * Removing files that I accidently added * Bugfix for cellrangerarc/mkgtf/main.nf * Rerun * Changes to tests/modules/nf-core/cellrangerarc/mkref/main.nf * Bugfix for python test data and cellrangerarc/count/main.nf * Iditot...
地址:Specifying Input FASTQ Files for cellranger-arc count -Software -Single Cell Multiome ATAC + Gene Exp. -Official 10x Genomics Support 数据质量控制 我们可以使用FastQC软件进行质量控制 FastQC软件可以参考:转录组之质量控制(FastQC)学习笔记通俗易懂版_YHC-BI的博客-CSDN博客 ...
Advanced Loupe Introduction Download Tutorial Cell Ranger ARC analyzes data generated by the Chromium Single Cell Multiome ATAC + Gene Expression assay to compute sequencing quality and application result metrics for each supported library type. Supported library types are "Gene Expression" and "Chroma...
zcat refdata-cellranger-arc-mm10-2020-A-2.0.0/genes/genes.gtf.gz|cat - egfp.gtf >genome.gtf 还需配置mm10_egfp.config文件: {organism:"mouse"genome:["mm10"]input_fasta:["new_ref/genome.fa"]input_gtf:["/new_ref/genome.gtf"]non_nuclear_contigs:["chrM"]input_motifs:"refdata-cellra...
Cell Ranger ARC's pipelines expose a user interface (UI) for monitoring progress through a web browser. By default, this UI is exposed at an operating system assigned port with a randomly-generated authentication token to restrict access. Specifying the--uiport=3600option when usingcellrangerwill...
According to Brett Olsen, Staff Computational Biologist at 10x Genomics, Cell Ranger ATAC v2 and Cell Ranger ARC v2 include “some substantial improvements to how we identify accessible regions of chromatin, or peaks, in our ATAC samples.” These peaks are a key component of many downs...