Table 1. CUTAC data quality is similar to that of the best ATAC-seq datasets.
Human K562 and H1 ES cell ATAC-seq datasets were downloaded from GEO, and Bowtie2 was used to map fragments to hg19. A sample of 3.2 million mapped fragments without Chr M was used for peak-calling by MACS2 to calculate FRiP values. Year of submission to GEO or SRA databanks is shown. % Chr M is percent of hg19-mapped fragments mapped to mitochondrial DNA.
| Sample | Source | Year | Read_type | Raw_reads | hg19-mapped | % Chr M | # Peaks | FRiP % |
|---|---|---|---|---|---|---|---|---|
| CUT&Tag-direct H1 | This study | 2020 | PE25 | 4,832,184 | 4,525,525 | 0.2 | 23,051 | 53 |
| CUT&Tag-direct K562 | This study | 2020 | PE25 | 3,252,490 | 3,144,253 | 2 | 20,555 | 41 |
| CUTAC H1 | This study | 2020 | PE25 | 2,770,901 | 2,734,092 | 1 | 16,848 | 25 |
| CUTAC K562 | This study | 2020 | PE25 | 5,973,063 | 4,785,931 | 3 | 14,381 | 22 |
| Omni-ATAC K562 SRR5657531-2 | Stanford | 2017 | PE75 | 4,407,706 | 3,181,110 | 13 | 16,737 | 20 |
| ATAC H1 GSM3677783 | Fred Hutch | 2019 | PE25 | 4,504,812 | 4,157,800 | 13 | 19,517 | 16 |
| ATAC K562 ENCFF123TMX | Stanford (ENCODE) | 2020 | PE100 | 43,473,266 | 23,942,024 | 9 | 14,369 | 11 |
| ATAC K562 GSM4083680 | U. Texas-Southwestern | 2019 | SE74 | 29,193,873 | 17,612,609 | 43 | 5894 | 8 |
| ATAC K562 GSM3452726 | Cornell U. | 2018 | PE36 | 86,907,625 | 83,038,866 | 24 | 1555 | 6.2 |
| ATAC K562 GSM4190694 | Keio U. | 2020 | PE60 | 15,363,855 | 14,067,803 | 79 | 1837 | 4.8 |
| ATAC H1 GSM4130883 | Stanford | 2020 | PE100 | 43,784,188 | 19,562,219 | 60 | 4289 | 3.2 |
| Fast-ATAC K562 SRR5657533-4 | Stanford | 2017 | PE75 | 6,702,558 | 4,677,843 | 8 | 2780 | 2.4 |
| ATAC K562 GSM4005278 | Penn State Hershey | 2020 | PE100 | 12,772,997 | 8,541,005 | 25 | 1691 | 2.1 |
| ATAC K562 GSM4130894 | Stanford | 2020 | PE100 | 45,122,834 | 19,021,462 | 86 | 449 | 1.4 |