运行 cellranger-atac mkfastq ,生成每个 GEM well 的 FASTQ 文件。对每个文库运行独立的 cellranger-atac count,使用cellranger-atac aggr将这些独立的 count 分析结果文件整合到一起,完成综合分析。 多个样本、多个 GEM wells、单个流动槽:这种场景...
cellranger count应该是Cell Ranger软件个人应用最广泛的部分。 1.3 cellranger aggr 组合两组数据(cellranger count的结果数据)。 1.4 cellranger reanalyze 设置不同参数重分析cellranger count或cellranger aggr的结果。 1.5 cellranger multi 处理Cell Multiplexing数据集。What is Cell Multiplexing? cellranger定量 ...
cellranger-arc aggris not designed for combining multiple sequencing runs of the same GEM Well. Instead, use the--librariesargument ofcellranger-arc countand add a row for each sequencing run. cellranger-arc aggronly accepts data generated by version 2.0+ ofcellranger-arc count. If you have...
cellranger count:输入 fastq 文件和 reference 数据,进行序列比对、细胞过滤、UMI 计数等,产生feature-barcode表达矩阵 cellranger aggr:将多个cellranger count 结果去批次/标准化后进行数据整合。 cellranger mkref:10x 单细胞转录组测序的参考基因组准备。 cellranger vdj:10x VDJ 数据文库分析,scTCR/BCR(T/B细胞...
64GB RAM(推荐128GB),最低配的64G允许cellranger aggr合并最多250k个细胞 1T硬盘 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04 1.下载 1.1 下载cellranger https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest 填写信息后,会给出两个软件(v3.1)下载链接,以及参考基因组(v3.0...
cellranger-atac count--id=sample345 \--reference=/opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0\--fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \--sample=mysample \--localcores=8\--localmem=64 cellranger-atac aggr cellranger-atac aggr--id=AGG123\--csv=AGG123_libraries.csv ...
Cell Ranger ARC v2 is getting a major upgrade. With the addition of two new pipelines, aggr and reanalyze, users can now analyze data from multiple samples together.Andrew Gottscho, Senior Scientific Writer, gave us some details on what this means for Single Cell Multiome ATAC + Gene...
Protospacer calling is performed again on the combined data included in the cellranger aggr run. CRISPR aggregation generates the crispr_analysis folder in the outs/ directory. The structure of the crispr_analysis folder is similar to the CRISPR outputs from count....
cellranger aggr --help cellranger aggr [OPTIONS] --id <ID> --csv <CSV> annotate Copy cloud auth setup Usage: Copy cellranger cloud auth --help Set up authentication Interactively walk through the process of setting up authentication. Running this command will prompt you to visit the 10x Ge...
If you have multiple libraries for the sample, you will need to runcellranger multion them individually, and then combine them withcellranger aggr. feature_typesRequired. The underlying feature type of the library (listedbelow). lanesOptional. The lanes associated with this sample, separated with...