scRNA-seq preprocessing

From Kallisto | Bustools workflow counttable to preprocessed Seurat object.

Installation

1. Install Miniconda.

2. Install Mamba

conda install mamba -n base -c conda-forge

3. Download the newest release of scRNA-seq or clone the repository.

git clone https://github.com/Rebecza/scRNA-seq.git

4. Create & activate environment.

cd scRNA-seq/envs
mamba env create -f kb_scrna_R_seurat3.yaml
conda activate kb_scrna_R_seurat3

5. Install RStudio (optional)

mamba install -n kb_scrna_R_seurat3 r::rstudio

Note: RStudio should be started from within the conda environment.

6. Running

• RStudio: Open kb_seurat_pp.rmd -> Fill parameters -> Knit
  
• Command-line: Run rmarkdown::render('kb_seurat_pp.rmd,....) from R console.

Running the alignment needed for scRNA-seq (and RNA Velocity)

The indexing and alignment for RNA Velocity can easily be performed with the scRNA-seq workflow of seq2science.