cellranger aggr

使用的样本每个都有4个RUN，因此对每个RUN单独count后，对四个count结果使用aggr合并

运行细胞游侠 aggr -软件 -单细胞基因表达 -官方 10x 基因组学支持 (10xgenomics.com)

cellranger-aggr
Aggregate data from multiple Cell Ranger runs

USAGE:
    cellranger aggr [FLAGS] [OPTIONS] --id <ID> --csv <CSV>

FLAGS:
        --nosecondary    Disable secondary analysis, e.g. clustering
        --dry            Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop
        --disable-ui     Do not serve the web UI
        --noexit         Keep web UI running after pipestance completes or fails
        --nopreflight    Skip preflight checks
    -h, --help           Prints help information

OPTIONS:
        --id <ID>               A unique run id and output folder name [a-zA-Z0-9_-]+
        --description <TEXT>    Sample description to embed in output files [default: ]
        --csv <CSV>             Path of CSV file enumerating 'cellranger count/vdj/multi' outputs
        --normalize <MODE>      Library depth normalization mode [default: mapped] [possible values: mapped, none]
        --jobmode <MODE>        Job manager to use. Valid options: local (default), sge, lsf, slurm or path to a
                                .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more
                                details on configuring the pipeline to use a compute cluster [default: local]
        --localcores <NUM>      Set max cores the pipeline may request at one time. Only applies to local jobs
        --localmem <NUM>        Set max GB the pipeline may request at one time. Only applies to local jobs
        --localvmem <NUM>       Set max virtual address space in GB for the pipeline. Only applies to local jobs
        --mempercore <NUM>      Reserve enough threads for each job to ensure enough memory will be available, assuming
                                each core on your cluster has at least this much memory available. Only applies to
                                cluster jobmodes
        --maxjobs <NUM>         Set max jobs submitted to cluster at one time. Only applies to cluster jobmodes
        --jobinterval <NUM>     Set delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes
        --overrides <PATH>      The path to a JSON file that specifies stage-level overrides for cores and memory.
                                Finer-grained than --localcores, --mempercore and --localmem. Consult
                                https://support.10xgenomics.com/ for an example override file
        --uiport <PORT>         Serve web UI at http://localhost:PORT

需要对多个需要合并的数据制作一个csv表格

创建聚合 CSV