occdn.limour.top/source/_posts/scvelo准备2：从cellranger得到loom文件.md

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title: scVelo准备2：从cellranger得到loom文件 tags: [] id: '1788' categories:

• - 原始数据
• - 拟时序

• • 生信

    date: 2022-05-05 18:01:41

    conda activate velocyto
    
    #!/bin/bash
    db=/opt/cellranger/refdata-gex-GRCh38-2020-A
    work=/home/jovyan/upload/zl_liu/data/data/res
    rmsk_gtf=/opt/cellranger/GRCh38_rmsk.gtf # 从genome.ucsc.edu下载 
    cellranger_gtf=${db}/genes/genes.gtf
    ls -lh $rmsk_gtf  $work $cellranger_gtf
    for sample in ${work}/*;
    do echo $sample
    velocyto run10x -m $rmsk_gtf $sample $cellranger_gtf
    done