|
Number of samples
|
2 |
2 |
2 |
2 |
2 |
2 |
2 |
3 |
3 |
2 |
|
Input reads (average per sample)
|
34,519,715 |
6,421,317 |
49,109,097 |
54,833,141 |
43,884,060 |
53,702,142 |
43,884,060 |
40,895,894 |
33,865,527 |
46,158,137 |
|
Alignment to unique sequences
|
|
|
|
|
|
|
|
|
|
|
| Aligned exactly 1 time (average per sample) |
21,455,086 |
3,097,077 |
28,275,831 |
28,626,785 |
28,035,327 |
23,326,061 |
21,945,541 |
22,882,234 |
27,123,469 |
30,651,658 |
| Aligned reads used for peak-calling (per sample) |
2,900,000 |
2,900,000 |
2,900,000 |
23,000,000 |
23,000,000 |
21,000,000 |
21,000,000 |
17,900,000 |
17,900,000 |
17,900,000 |
| Regional peaks identified by peakranger 1.16 (average for condition) |
7,746 |
8,868 |
7,376 |
17,116 |
421 |
128,518 |
100,884 |
145,322 |
27,544 |
65,629 |
| Significantly different peaks identified by DiffBind |
224 |
|
3,844 |
9,505 |
8,480 |
|
| DiffBind result confirmed by visual inspection |
124 |
|
random sample of 100 peaks for each condition(33–50% confirmed by 2 independent observers) |
|
| EpiChIP peaks with signal at FDR 0.01 (per condition) |
3,598 |
3,566 |
3,954 |
|
|
|
|
4,801 |
4,370 |
5,024 |
|
Alignment to repetitive sequences
|
|
|
|
|
|
|
|
|
|
|
| Aligned exactly 1 time (average per sample) |
1,326,620 |
242,000 |
|
3,805,162 |
3,091,945 |
3,881,193 |
3,612,100 |
3,999,829 |
4,554,097 |
|
| Random sample used for DESeq |
220,000 |
220,000 |
|
2,900,000 |
2,900,000 |
3,400,000 |
3,400,000 |
3,900,000 |
3,900,000 |
|
