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 ...
By default,cellranger-arcwill use all the cores available on your system to execute pipeline stages. You can specify a different number of cores to use with the--localcoresoption; for example,--localcores=16will limitcellranger-arcto using up to sixteen cores at once. Similarly,--localmemwi...
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 + Gen...
Cell Ranger主要的流程有:拆分数据 mkfastq、细胞定量 count、定量组合 aggr、调参reanalyze,还有一些小工具比如mkref、mkgtf、upload、sitecheck、mat2csv、vdj、mkvdjref、testrun。 但是,大概率上,我们只需要使用它的定量流程,就是 cellranger count 命令,教程在consult Running 10x Pipelines on FASTQ Files,主要...
cellranger aggr --help cellranger aggr [OPTIONS] --id <ID> --csv <CSV> ArgumentDescription --id Required. A unique run ID string: e.g. AGG123 --output-dir Optional. Path to a custom output directory for storing the results of the run. When this argument is specified, the output...
cellranger-atac aggrdoes not perform a cell-calling step, it simply aggregates the cell calls as encoded insinglecell.csvfrom each input job into a final set of cell calls. A successful run will conclude with a message like this:
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 ...
ARC-v1: For analyzing the Gene Expression portion of Multiome data. Note: If Cell Ranger auto-detects ARC-v1 chemistry, an error is triggered. 3' Cell Multiplexing only These [gene-expression] options only apply to 3' Cell Multiplexing data analysis. FieldDescription min-assignment-confidence...