velocyto-scRNAseq速率的计算

介绍： https://cloud.tencent.com/developer/article/1607921

安装：注意：velocyto 需要 python 版本>=3.6.0

git clone https://github.com/velocyto-team/velocyto.py.git
cd velocyto.py
pip install -e .  # note the trailing dot

其他安装方式 https://velocyto.org/velocyto.py/install/index.html#install

使用方法以10X为例

1.Running the CLI

Usage: velocyto run10x [OPTIONS] SAMPLEFOLDER GTFFILE
          Runs the velocity analysis for a Chromium 10X Sample
          10XSAMPLEFOLDER specifies the cellranger sample folder
          GTFFILE genome annotation file
        Options:
          -s, --metadatatable FILE        Table containing metadata of the various samples (csv fortmated rows are samples and cols are entries)
          -m, --mask FILE                 .gtf file containing intervals to mask
          -l, --logic TEXT                The logic to use for the filtering (default: Default)
          -M, --multimap                  Consider not unique mappings (not reccomended)
          -@, --samtools-threads INTEGER  The number of threads to use to sort the bam by cellID file using samtools
          --samtools-memory INTEGER       The number of MB used for every thread by samtools to sort the bam file