Table 2.
snATACseq quality control rules
| snATACseq Rules | Not Pass | Pass | Good |
|---|---|---|---|
| Fraction of transposition events in peaks in cells | <0.05 | [0.05,0.2) | >0.2 |
| Confidently mapped read pairs | <0.5 | [0.5, 0.75) | >0.75 |
| Q30 bases in read 1 | <55% | [55%–65%) | >65% |
| Q30 bases in read 2 | <55% | [55%–65%) | >65% |
| Median high-quality fragments per cell | <500 | ≥500 | ≥500 |
| TSS enrichment score | <2 | [2,4) | ≥4 |
| Additional QC reference metrics | Caution | Pass | Good |
| Nucleosome-free region (NFR) peak | No | Yes | Yes |
| Mononucleosome peak | No | Yes | Yes |
Presented in the table are the QC metrics rules used to assess sequencing quality of the snATACseq libraries.