This is a pipeline to process single-cell RNA data from 10X multiome.
Note: If your data is single-cell RNA only from the 10X, you have to run cellranger by yourself.
After running cellranger, you can start from 4_create_StObject.sh
In order to run this pipeline, you have to install the following packages:
Seurat: https://github.com/satijalab/seurat
optparse: https://www.rdocumentation.org/packages/optparse/versions/1.7.3
SeuratWrappers: https://github.com/satijalab/seurat-wrappers
DoubletFinder: https://github.com/chris-mcginnis-ucsf/DoubletFinder
(optional): if you want to do batch correction using harmony or Liger
harmony: https://github.com/immunogenomics/harmony
rliger: https://github.com/welch-lab/liger
The the exection file is the file with the ".sh" extension in ./exe folder.
The number of each file indicating the order of analysis.
The scripts used in the exection file are saved under the ./src folder.