Quality control

After loading a single-sample dataset, Asc-Seurat shows QC violin plots for:

  • nFeature_RNA: genes detected in each cell.

  • nCount_RNA: molecules detected in each cell.

  • percent.mt: percentage of transcripts matching the mitochondrial pattern.

Filtering mode

The filtering panel has two modes:

  • No filtering keeps all loaded cells for normalization.

  • Use filtering thresholds applies minimum genes, maximum genes, and maximum mitochondrial percentage cutoffs.

The suggested threshold values are calculated from the loaded dataset as median plus or minus three median absolute deviations (MADs), with safeguards for valid ranges. These defaults are meant as a starting point, not a substitute for reviewing the violin plots.

Doublet removal

Doublet detection is independent from metric filtering. The Detect and remove doublets (scDblFinder) checkbox is available in both filtering modes:

  • With No filtering, Asc-Seurat keeps all cells except predicted doublets when the checkbox is enabled and Apply Filters is run.

  • With Use filtering thresholds, Asc-Seurat first applies the QC thresholds and then removes predicted doublets if requested.

If doublet removal is not selected and No filtering is active, you can proceed directly to Run Normalization + PCA.

Downloads

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