下载安装CellRanger
- 下载
curl -o cellranger-7.1.0.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-7.1.0.tar.gz?Expires=1695057805&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci03LjEuMC50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2OTUwNTc4MDV9fX1dfQ__&Signature=mgfbVO4t-SDiQBfplG2H-6GzTTJEYeusFjVrlA077ficI3jR8sRM9LL4GP0vZf3jstfK2X2ktdNeY8U0ceiK0sIlCA0UrYJnP8iq290SSQimdUlQ~vUongSy~Nkeczatjl~Yin5NUhwPvMQnlpfx3caOt4MiWhLMbkpXp-I6v8Dyo8E8q8c0v2rPs~Wr~4KjSWaBvir4criW4kBeezgptSc7YStuKbnpuOHe~hkOWCwp8yN52AYKkKn~YmM9gkqKAjbGSPEdU7PIvqNDtjTNvPxmYN2R33nRvZ2AYTDBn7JbybSnnZTdznr1s7g~5oB4SQafQPzxUWR8338kgbvDgg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
- 解压并安装
tar -zxvf cellranger-7.1.0.tar.gz
cd cellranger-7.1.0
pwd
# 添加到环境变量
vi ~/.bashrc
export PATH=$PATH:/home/txm/software/cellranger-7.1.0
source ~/.bashrc
- 运行测试
cellranger testrun --id=check_install
下载CellRanger所需的参考基因组
# hg38
curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
# mm10
curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
# hg38 & mm10
curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-and-mm10-2020-A.tar.gz
下载完记得使用tar -zxvf解压
cellranger count：基因定量
cellranger count --id=TAO1 \
--transcriptome=/home/txm/genome/cellranger/refdata-gex-GRCh38-2020-A \
--fastqs=/home/txm/project/TAO/data/CRM/TAO1 \
--sample=TAO1 \
--localcores=40 \
--localmem=200
fastq命名规则：
[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz
eg:
HC1_S1_L001_R1_001.fastq.gz
HC1_S1_L001_R2_001.fastq.gz
cellranger aggr：合并表达矩阵
CRM_df <- data.frame(sample_id = c('HC1','HC2','TAO1','TAO2','TAO3','TAO4'),
molecule_h5 = c('/home/txm/project/TAO/data/CRM/HC1/HC1/outs/molecule_info.h5',
'/home/txm/project/TAO/data/CRM/HC2/HC2/outs/molecule_info.h5',
'/home/txm/project/TAO/data/CRM/TAO1/TAO1/outs/molecule_info.h5',
'/home/txm/project/TAO/data/CRM/TAO2/TAO2/outs/molecule_info.h5',
'/home/txm/project/TAO/data/CRM/TAO3/TAO3/outs/molecule_info.h5',
'/home/txm/project/TAO/data/CRM/TAO4/TAO4/outs/molecule_info.h5'))
write.csv(CRM_df,'/home/txm/project/TAO/data/CRM/CRM_df.csv',row.names = F,quote = F)
cellranger aggr --id=aggr \
--csv=/home/txm/project/TAO/data/CRM/CRM_df.csv \
--normalize=mapped
参考
下载：https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
定量：https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
