Cellranger的下载、安装

1. Cellranger的下载

此处以10X官网上最新的Cellranger版本为例下载，网址如下：

wget -O cellranger-6.1.2.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-6.1.2.tar.gz?Expires=1635685923&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci02LjEuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2MzU2ODU5MjN9fX1dfQ__&Signature=IdVssu4uhoH2HQcJ6Fc66z~Wcf8x09lfKU0g2ARgKBjB11bc3IroxYh3ZeExzOJzZkTNjuIo94pRmjMZ9GjjIzOwteLBmKU83nA2JUbUPW28CAfvWFiuTDme94Ty68XUuYEXNPYJA88YP3OyMGgh2T4KKAdYRen2GDjmu~MvUZdNtOniTsWNbT0IQBeoGI8DE1Rcl1QLiK90uiCcw-aXOsTc~w4OQZiEUj0vd5N~KgpUWHdd4Nzy9Y0~SP~DBFkSYYcKEZ6qOUnq~BUDOq5QMcsPfz244WNaFfnUkLnF2tnzXQsjYvDm7obs2iWUGRXgnODcJ7B9UXRrLG5wDfdI7A__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

下载至某一文件夹，本例中以下载至software文件夹为例。

cd ~/software

之后，进行解包、解压缩。

tar -zxvf cellranger-6.1.2.tar.gz

2. 添加Cell Ranger到$PATH

export PATH=~/download/cellranger-6.1.2:$PATH

检验是否添加到$PATH:

which cellranger

输出如下：

/home/user_name/software/cellranger-6.1.2/cellranger # user_name是所使用服务器用户的名字

也可以添加到.bashrc，这样下次登陆就不用再次export了，切换到家目录下,

vi .bashrc 

将下方这句添加到.bashrc文件中，

export PATH=~/download/cellranger-6.1.2:$PATH

更新一下.bashrc文件。

source .bashrc

3. 执行 sitecheck

cellranger sitecheck > sitecheck.txt

发送sitecheck.txt到10X的支持团队

cellranger upload your_email@email.com sitecheck.txt

输出如下，

Getting upload information...
Uploading file...
Size: 17,676 bytes
100% [=================================>] 17,676   0.28Mb/s  eta 0m  0s  
Upload complete!

4. Cellranger试运行

cellranger testrun --id=tiny

试运行结果输出如下，

Pipestance completed successfully!