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What are the QC metrics for scFAST-seq data? How should data quality be evaluated?
2026-06-23
Answer:
scFAST-seq data should be evaluated using both standard scRNA-seq metrics and scFAST-seq-specific metrics.
1. Standard metrics (same as 3' transcriptome):
- Median genes per cell
- UMI counts
- Mitochondrial gene percentage
2. scFAST-seq specific metrics:
Metric | Acceptance Threshold |
Reads covering gene body middle region | >55% |
ACTB coverage (positions with ≥0.2× mean depth) | >70% |
rRNA fraction | <10% |
3. Coverage uniformity (key indicator):
- Use a housekeeping gene (e.g., ACTB)
- Map reads with valid cell barcodes across the full gene body
- Divide gene into windows and calculate coverage depth
- Proportion of regions with ≥20% of mean depth should be >70%
Indicates sufficiently uniform coverage
4. rRNA assessment: rRNA fraction should be <10% (Human / Mouse)
Indicates effective rRNA blocking and high proportion of informative mRNA reads
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