Single-cell-RNA-seq-of-the-CRISPR-engineered-endogenous-tauopathy-model
Output Details
Description
scRNA-seq data analysis workflow
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:
Run Rscript hassan_merged_seurat.r -l expectedCells/ -s scrublet/ -k outdir/ -j hassan2022 -r refdir path_to_ref_directory
This will generate Seurat results.
Step6:
Proceed with the trajectory and the fly phone DB analysis, using their respective code, on the integrated Seurat object.
Step7:
pySCENIC
Step8:
OmicsIntegrator
