# 通过conda安装纯净环境的velocyto

## cellranger

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

https://www.jianshu.com/p/1e7acde1a318

https://mp.weixin.qq.com/s/TJsdj7qesZGlvmEkNLAy0A

GRCh38_rmsk.gtf.gz：https://genome.ucsc.edu/cgi-bin/hgTables

- cd /opt/cellranger
- wget <Cell Ranger>
- wget <References>
- tar -xzvf cellranger-6.1.2.tar.gz
- tar -xzvf refdata-gex-GRCh38-2020-A.tar.gz
- 下载 GRCh38_rmsk.gtf.gz 上传阿里云盘
- ./aliyunpan
- login
- d GRCh38_rmsk.gtf.gz -saveto /opt/cellranger
- gunzip GRCh38_rmsk.gtf.gz
- export PATH=/opt/cellranger/cellranger-6.1.2:$PATH
- cellranger sitecheck > sitecheck.txt
- cellranger upload xxx@fudan.edu.cn sitecheck.txt
- cellranger testrun –id=tiny
- cellranger upload xxx@fudan.edu.cn tiny/tiny.mri.tgz

## velocyto

http://velocyto.org/

http://velocyto.org/velocyto.py/install/index.html#install

- conda create -n velocyto -c conda-forge python=3.7 -y
- conda activate velocyto
- conda install numpy scipy cython numba matplotlib scikit-learn h5py click -y
- pip install pysam
- pip install velocyto
- velocyto –help
- conda install -c bioconda samtools=1.15.1 -y

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通过conda安装纯净环境的velocyto
https://occdn.limour.top/1779.html
Author
Limour
Posted on
May 1, 2022
Licensed under
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