scRNA-seq data analysis Tingting Zhao 05092022 Step1: bash cellranger_mkfastq.sh This will generate fastq files. Step2: bash cellranger_count_submission.sh This will call another bash file “cellranger_count.sh” and generate count tables Step3: bash run_scrublet_multi.sh This will call “scrublet_multi.py” and generate scrublet results. If seeing error refer to “scrublet_multi_conditional.py”. Step4: bash scRNA_seq.sh This will call “seurat_individual.R” and generate QC plots for each sample. Step5: vanitha_merged.rmd in Rstudio This will generate Seurat results.