ScDblFinder

scDblFinder is a transcriptome-based doublet detecting method that uses doublet simulation from droplets in the dataset to identify doublets. We have provided a wrapper script that takes common arguments for ScDblFinder and also provide example code for you to run manually if you prefer.

Data

This is the data that you will need to have prepare to run ScDblFinder:

Required

  • A counts matrix ($COUNTS)

    • The directory path containing your cellranger counts matrix files (directory containing barcodes.tsv, genes.tsv and matrix.mtx or barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

      or

    • h5 file (filtered_feature_bc_matrix.h5)

      • If you don’t have your data in this format, you can run ScDblFinder manually in R and load the data in using a method of your choosing.

  • Output directory ($SCDBLFINDER_OUTDIR)

    • If you don’t provide an $SCDBLFINDER_OUTDIR, the results will be written to the present working directory.

Run ScDblFinder

You can either run ScDblFinder with the wrapper script we have provided or you can run it manually if you would prefer to alter more parameters.

singularity exec Demuxafy.sif scDblFinder.R -o $SCDBLFINDER_OUTDIR -t $COUNTS

ScDblFinder Results and Interpretation

After running the ScDblFinder with the wrapper script or manually you should have two files in the $SCDBLFINDER_OUTDIR:

.
├── scDblFinder_doublets_singlets.tsv
└── scDblFinder_doublet_summary.tsv

Here’s a more detaild description of each of those files:

  • scDblFinder_doublet_summary.tsv

    • A sumamry of the number of singlets and doublets predicted by ScDblFinder.

      Classification

      Droplet N

      doublet

      3323

      singlet

      17659

  • scDblFinder_doublets_singlets.tsv

    • The per-barcode singlet and doublet classification from ScDblFinder.

      Barcode

      scDblFinder_DropletType

      scDblFinder_Score

      AAACCTGAGATAGCAT-1

      singlet

      0.0033526041079312563

      AAACCTGAGCAGCGTA-1

      doublet

      0.9937564134597778

      AAACCTGAGCGATGAC-1

      singlet

      5.045032594352961e-

      AAACCTGAGCGTAGTG-1

      singlet

      0.007504515815526247

      AAACCTGAGGAGTTTA-1

      singlet

      0.00835108570754528

      AAACCTGAGGCTCATT-1

      singlet

      0.028838597238063812

      AAACCTGAGGGCACTA-1

      doublet

      0.9985504746437073

      AAACCTGAGTAATCCC-1

      singlet

      0.005869860760867596

Merging Results with Other Software Results

We have provided a script that will help merge and summarize the results from multiple softwares together. See Combine Results.

Citation

If you used the Demuxafy platform for analysis, please reference our paper (REFERENCE) as well as ScDblFinder.