# scVelo准备1：cellranger

## 重命名R1、R2

data
├── hPB003
│ ├── hPB003_S1_L001_R1_001.fastq.gz
│ └── hPB003_S1_L001_R2_001.fastq.gz
├── hPB004
│ ├── hPB004_S1_L001_R1_001.fastq.gz
│ └── hPB004_S1_L001_R2_001.fastq.gz
├── hPB005
│ ├── hPB005_S1_L001_R1_001.fastq.gz
│ └── hPB005_S1_L001_R2_001.fastq.gz
├── hPB006
│ ├── hPB006_S1_L001_R1_001.fastq.gz
│ └── hPB006_S1_L001_R2_001.fastq.gz
└── hPB007
├── hPB007_S1_L001_R1_001.fastq.gz
└── hPB007_S1_L001_R2_001.fastq.gz

## 运行Cell Ranger

https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247495226&idx=1&sn=baff3b7bcf2091a2a658c046dce421cd&scene=21#wechat_redirect

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    #!/bin/bash
    export PATH=/opt/cellranger/cellranger-6.1.2:$PATH
    db=/opt/cellranger/refdata-gex-GRCh38-2020-A
    data=/home/jovyan/upload/zl_liu/data/data/data
    work=/home/jovyan/upload/zl_liu/data/data/res
    mkdir $work
    cd $work
    for sample in ${data}/*;
    do echo $sample
    sample_res=${sample##*/}
    cellranger count --id=$sample_res \
    --localcores=4 \
    --transcriptome=$db \
    --fastqs=$sample \
    --sample=$sample_res \
    --expect-cells=5000
    done

生信 拟时序
scVelo准备1：cellranger
https://occdn.limour.top/1783.html
Author
Limour
Posted on
May 1, 2022
Licensed under
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