Here includes raw data process, annotation, and how to further analysis scRNA data for sQTL
At first, you need to download reference genome and its gtf file, since our data comes from human, you can download them from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Next, you can use the count function to generate the files for Seurat:
nohup bash cellranger_count.sh &
Here, we recommend you to annotate the cell cluster manually, and Seurat.R includes how to process data coming from cellranger and get the files for annotation.