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Winuthayanon Lab How to analyze single‐cell RNA‐seq

Setup and Install Velocyto

Setup and Install Velocyto

To run VeloCyto, you will need Python >=3.6.0 (we have no plans to support python<=3.5). We recommend using anaconda and the conda command to install dependencies

cd $HOME/opt

Accept all defaults for “Do you wish the installer to initialize Anaconda3 by running conda init?” say Yes.

Verify that conda is installed by running it in the Terminal:

conda update -- all and conda upgrade --all

Building and installing

cd $HOME/opt
tar jxvf samtools-1.10.tar.bz2
cd $HOME/opt/samtools-1.10
./configure --prefix=$HOME/opt/samtools
make install
export PATH=$HOME/opt/samtools/bin:$PATH

Run the following command to make sure you have all the dependencies correctly installed:

conda install numpy scipy cython numba matplotlib scikit-learn h5py click

If there are issues with conda try running it in the Terminal:

pip install velocyto

Verify the installation by running in the Terminal:

velocyto --help

Usage: velocyto [OPTIONS] COMMAND [ARGS]…

–version Show the version and exit.
–help Show this message and exit.

run Runs the velocity analysis outputting a loom file
run10x Runs the velocity analysis for a Chromium Sample
run-dropest Runs the velocity analysis on DropEst preprocessed data
run-smartseq2 Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)
tools helper tools for velocyto