Table 1 Description of 8 approaches used to calculate ATAC-seq differential accessibility
| # | Genomic regions | Tool | Normalization | DA testing |
|---|---|---|---|---|
| I | MACS2 [27] | DiffBind [29] | Full library size | DESeq2 [31] |
| II | MACS2 [27] | DiffBind [29] | Reads in peaks | DESeq2 [31] |
| III | MACS2 [27] | csaw [28] | TMM [34] | edgeR [30] |
| IV | MACS2 [27] | csaw [28] | Loess | edgeR [30] |
| V | csaw [28] | csaw [28] | TMM [34] | edgeR [30] |
| VI | csaw [28] | csaw [28] | Loess | edgeR [30] |
| VII | MACS2 [27] | csaw [28] | voom [32] | Log2cpm | limma [33] |
| VIII | MACS2 [27] | csaw [28] | voom [32] | Quantile [35] | limma [33] |