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
• wget
• 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