Table 2 Quality metrics of ATAC-seq libraries. Non-redundant read fraction (NRF) measures library complexity, Fraction of reads in peaks (FRiP) measures signal-to-noise ratio, and synthetic Jensen-Shannon distance (sJSD) measures divergence between ATAC-seq signal and a uniform distribution
From: A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Species | Tissue | Replicate | NRF | FRiP | sJSD |
|---|---|---|---|---|---|
Cattle | Adipose | A | 0.43 | 9.82 | 0.34 |
Adipose | B | 0.79 | 15.04 | 0.34 | |
Cerebellum | B | 0.60 | 42.53 | 0.48 | |
Brain Cortex | A | 0.35 | 30.16 | 0.48 | |
Brain Cortex | B | 0.45 | 40.80 | 0.49 | |
Hypothalamus | A | 0.51 | 43.67 | 0.50 | |
Hypothalamus | B | 0.51 | 11.97 | 0.37 | |
Liver | A | 0.42 | 37.99 | 0.50 | |
Liver | B | 0.44 | 28.17 | 0.44 | |
Lung | A | 0.83 | 37.63 | 0.45 | |
Lung | B | 0.80 | 44.26 | 0.48 | |
Muscle | A | 0.82 | 40.77 | 0.50 | |
Muscle | B | 0.85 | 41.77 | 0.51 | |
Spleen | A | 0.35 | 21.29 | 0.42 | |
Spleen | B | 0.68 | 35.24 | 0.45 | |
Pig | Adipose | A | 0.82 | 5.21 | 0.40 |
Adipose | B | 0.81 | 4.12 | 0.40 | |
Cerebellum | A | 0.49 | 43.05 | 0.46 | |
Cerebellum | B | 0.64 | 41.49 | 0.47 | |
Brain Cortex | A | 0.63 | 40.65 | 0.48 | |
Brain Cortex | B | 0.50 | 44.53 | 0.46 | |
Hypothalamus | A | 0.51 | 36.85 | 0.49 | |
Hypothalamus | B | 0.43 | 37.76 | 0.44 | |
Liver | A | 0.32 | 55.38 | 0.52 | |
Liver | B | 0.48 | 49.25 | 0.49 | |
Lung | A | 0.81 | 31.21 | 0.43 | |
Lung | B | 0.83 | 36.87 | 0.46 | |
Muscle | A | 0.75 | 58.16 | 0.62 | |
Muscle | B | 0.71 | 61.94 | 0.65 | |
Spleen | A | 0.85 | 29.41 | 0.43 | |
Spleen | B | 0.86 | 22.70 | 0.38 |