单细胞测序分析软件Cell Ranger安装教程(Linux版)

使用Cell Ranger处理10x Genomics测序数据是一个多步骤的过程，涉及到数据的质量控制、读段的映射到参考基因组、识别和定量单细胞中的转录本。

官方教程

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in

下载基因组参考

地址: https://www.10xgenomics.com/support/software/cell-ranger/downloads

下载Linux版本:

wget -O cellranger-8.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-8.0.1.tar.gz?Expires=1729308219&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=eKPqcBP98w~V69a-V0LiWvNpisjFESYFT80bF4gfqUZbsQor4SIUcSfjQn3RN4uz3MU11i1dcLLfXtqvToEijaNYviVdjWc-kIIEW5p2ySi6dsU2z1EcDaUb-9-oBS2TALfMSo9Y9QOJ2ts3PDgYRNc9hCkdGVQpF9J9xf973pSVmkq9OII1grVtqdbvJ6MCA3DW9X~AEDQr1ncbyRpctLQmMASEPOpIsHT83SEWu7LENL8mw6b1NB7jr1CMSS1G81jZgSv-MnwcE3NOv3VbHwcDJU6f3uBdXMa7Y3hx3FYF43~2NRHsgrEJqjFeWkLk-08iBCjhEC0aYX7J40k1Dw__"

人的参考：

Human reference (GRCh38) dataset required for Cell Ranger（11G）

$ curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz

查看md5sum值:

$ md5sum refdata-gex-GRCh38-2020-A.tar.gz 
dfd654de39bff23917471e7fcc7a00cd  refdata-gex-GRCh38-2020-A.tar.gz

鼠的参考：

Mouse reference dataset required for Cell Ranger（9.7G）

$ curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz

人和鼠的参考：

Human reference (GRCh38) and mouse dataset required for Cell Ranger（9.9G）

$ curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-and-mm10-2020-A.tar.gz

Cell Ranger安装

解压

$ sudo tar -vxzf cellranger-8.0.1.tar.gz -C /opt/

配环境

$ vim ~/.bashrc

或者

vim /etc/profile

添加这个

export PATH=/opt/cellranger-8.0.1/bin:$PATH

如果用bash执行这个

$ source ~/.bashrc

安装成功（数据还是7.2.0版本的下面的就不跟着更新了意思到了就行）；

$ cellranger

cellranger cellranger-7.2.0

Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data

Usage: cellranger <COMMAND>

Commands:
  count           Count gene expression and/or feature barcode reads from a single sample and GEM well
  multi           Analyze multiplexed data or combined gene expression/immune profiling/feature barcode data
  multi-template  Output a multi config CSV template
  vdj             Assembles single-cell VDJ receptor sequences from 10x Immune Profiling libraries
  aggr            Aggregate data from multiple Cell Ranger runs
  reanalyze       Re-run secondary analysis (dimensionality reduction, clustering, etc)
  mkvdjref        Prepare a reference for use with CellRanger VDJ
  mkfastq         Run Illumina demultiplexer on sample sheets that contain 10x-specific sample index sets
  testrun         Execute the 'count' pipeline on a small test dataset
  mat2csv         Convert a gene count matrix to CSV format
  mkref           Prepare a reference for use with 10x analysis software. Requires a GTF and FASTA
  mkgtf           Filter a GTF file by attribute prior to creating a 10x reference
  upload          Upload analysis logs to 10x Genomics support
  sitecheck       Collect linux system configuration information
  help            Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

bajiu

单细胞测序分析软件Cell Ranger安装教程(Linux版)

下载基因组参考

Cell Ranger安装