scVelo准备1:cellranger

发布于 2022-05-01  115 次阅读


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

#!/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

 


一枚爱好探索的医学生