Login to tadpole and navigate to your directory on the share space.

cd /share/workshop/adv_scrna/$USER

srun -t 1-00:00:00 -c 4 -n 1 --mem 16000 --partition production --account adv_scrna_workshop --reservation adv_scrna_workshop  --pty /bin/bash

RNA Velocity measurement using Velocyto

RNA velocity is the time derivative of the gene expression state, (La Manno et al., 2018) allows for the inference of the dynamic patterns in scRNA-seq data sets, by looking at the abundance of unspliced and spliced mRNA RNA in each cell, and modelling using a system of ordinary differential equations.

From a quantification point of view, RNA velocity analysis requires the generation of two count matrices, representing the spliced/processed (exonic) and unspliced/unprocessed RNA (intronic).

RNA velocity is a high-dimensional vector that predicts the future state of a cell on a timescale of hours.

Example dataset

We’ll use the example dataset from Mapping Comparison section from the paper, sample 654_small

“Single-Cell RNA-seq Reveals Profound Alterations in Mechanosensitive Dorsal Root Ganglion Neurons With Vitamin E Deficiency”

and the cellranger count results folder from the Mapping section.

/share/workshop/adv_scrna/msettles/scrnaseq_processing/654_small

cd /share/workshop/adv_scrna/$USER/scrnaseq_processing

we also need the gtf file used in creating the reference, which should be here:

/share/workshop/adv_scrna/msettles/scrnaseq_processing/Reference/Mus_musculus.GRCm38.100.filtered.gtf .

Next lets install the software velocyto

To install velocyto (a python application) we are going to use conda and a virtual environment

cd /share/workshop/adv_scrna/$USER
module load anaconda3
conda create -p velocyto
conda activate /share/workshop/adv_scrna/$USER/velocyto

If the environment ‘activated’ properly, than your prompt should look something like this.

(/share/workshop/adv_scrna/msettles/velocyto) msettles@tadpole:/share/workshop/adv_scrna/msettles$

If not you can try to initialize your bash

kinit
conda init bash
source /home/$USER/.bashrc
conda activate /share/workshop/adv_scrna/$USER/velocyto

Once your conda environment is properly activated you can then install the softare.

# install prerequisites
conda install numpy scipy cython numba matplotlib scikit-learn h5py click
# install velocyto
pip install velocyto

and then test the installation

velocyto --help

It is also recommended to use a repetative sequence mask file, this is easiest to obtain from the UCSC genome browser.

You want to download the mask in gtf format. Unfortunately, Ensembl doesn’t provide a gtf file for th repeat sequences and we’d have to generate one ourselves (write a script to do so) which is beyond the scope of this workshop.

Running Velocyto on Cellranger output

Lets first take a look at the help doc for run10x

velocyto run10x --help

Ok, now we are ready to run this on our sample

cd /share/workshop/adv_scrna/$USER/scrnaseq_processing
velocyto run10x  654_small References/Mus_musculus.GRCm38.100.filtered.gtf

Output

Velocyto run10x simply produces a folder called velocyto in the sample directory with a single loom file in it, which contains the needed matrices for the analysis.

The output folder 654_small, now has a new folder called velocyto

drwxrwsr-x 5 msettles biocore   20 May 28 07:22 .
drwxrwsr-x 3 msettles biocore    4 May 28 07:17 ..
-rw-rw-r-- 1 msettles biocore 4.2M May 28 06:29 654.mri.tgz
-rw-rw-r-- 1 msettles biocore  287 May 28 06:29 _cmdline
-rw-rw-r-- 1 msettles biocore  66K May 28 06:29 _filelist
-rw-r--r-- 1 msettles biocore 969K May 28 06:29 _finalstate
-rw-r--r-- 1 msettles biocore  719 May 28 06:29 _invocation
-rw-r--r-- 1 msettles biocore    5 May 28 06:29 _jobmode
-rw-r--r-- 1 msettles biocore  69K May 28 06:27 _log
-rw-r--r-- 1 msettles biocore  66K May 28 06:29 _mrosource
drwxrwsr-x 5 msettles biocore   14 May 28 06:28 outs
-rw-r--r-- 1 msettles biocore 577K May 28 06:29 _perf
drwxrwsr-x 6 msettles biocore    6 May 28 06:26 SC_RNA_COUNTER_CS
-rw-rw-r-- 1 msettles biocore  17K May 28 06:29 _sitecheck
-rw-r--r-- 1 msettles biocore    2 May 28 06:29 _tags
-rw-r--r-- 1 msettles biocore   51 May 28 06:27 _timestamp
-rw-r--r-- 1 msettles biocore   36 May 28 06:29 _uuid
-rw-r--r-- 1 msettles biocore 132K May 28 06:27 _vdrkill
drwxrwsr-x 2 msettles biocore    3 May 28 08:50 velocyto    <-----
-rw-r--r-- 1 msettles biocore   61 May 28 06:27 _versions

and inside that folder is the loom file.

drwxrwsr-x 2 msettles biocore   3 May 28 08:50 .
drwxrwsr-x 5 msettles biocore  20 May 28 07:22 ..
-rw-rw-r-- 1 msettles biocore 56M May 28 08:52 654.loom

I expect that the 654_small dataset will fail as their aren’t enough reads, but on a full dataset it produces the loom file.

More reading

A detailed study of the impact of quantification on RNA velocity estimates and interpretation, see Soneson et al., 2020.