This website uses cookies so that we can provide you with the best user experience possible. Cookie information is stored in your browser and performs functions such as recognising you when you return to our website and helping our team to understand which sections of the website you find most interesting and useful.
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