cellranger-arc count--id=test_sample \--reference=/home/guoyuh/biosoft/refdata-cellranger-arc-GRCh38-2020-A-2.0.0\--libraries=libraries.csv \--localcores=16\--localmem=64 此测试数据集存在bug,这一步没有跑通。 不过如果运行成功,生成的文件将可用于下游分析。 单细胞转录组下游分析常用Seurat或...
运行代码: cellranger-arc count--id=sample345 \--reference=/opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0\--libraries=/home/jdoe/runs/libraries.csv \--localcores=40\--localmem=100
通常我们用到的是count定量 代码语言:javascript 复制 cellranger-arc count --id=sampleid \ --reference=/opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \ --libraries=/home/jdoe/runs/libraries.csv \ --localcores=16 \ --localmem=64 --id #运行ID符,同时也是pipline的输出结果目录。可以使用...
The computational pipeline cellranger-arc count for Single Cell Multiome ATAC + Gene Expression involves the following analysis steps:The main components of cellranger-arc count include:ATAC Matrix Computer: ATAC FASTQs → Peak-Barcode Matrix
Run cellranger-arc count To generate single cell feature counts and secondary analyses for a single library, runcellranger-arc countwith the following arguments. For a complete listing of the arguments accepted, see theCommand Line Argument Referencebelow, or runcellranger-arc count --help. ...
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...
$cellranger-arc count--id=sample345\--reference=/opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0\--libraries=/home/jdoe/runs/libraries.csv\--localcores=16\--localmem=64--noexitMartian Runtime - v4.0.5 Serving UI at http://host.example.com:3600 ...
Median genes per cellThe median number of genes detected per cell barcode. Detection is defined as the presence of at least one UMI count. Median UMI counts per cellThe median number of UMI counts per cell barcode. Percent duplicatesThe fraction of reads originating from an already-observed ...