Integrated quality control

After multi-sample integration, Asc-Seurat shows integration QC metrics and an optional additional filtering panel. This step is intended for post-integration cleanup after you have already reviewed each sample individually.

The integrated QC violin plot shows:

• nFeature_RNA: genes detected in each cell.

• nCount_RNA: molecules detected in each cell.

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

Choose No additional filtering to cluster the integrated object as created. Choose Use filtering thresholds to apply another round of minimum genes, maximum genes, and maximum mitochondrial percentage cutoffs.

The integration tab also shows an elbow plot after integration. Use it to choose the number of PCs for downstream clustering.

Download controls are collapsed by default. Expand Download options to choose plot size, resolution, and file type.