chipnexus data from julias lab
Pipeline version: v1.1.6
Report generated at 2020-01-29 02:32:52
Paired-end: False
Pipeline type: ChIP-nexus
Genome: mm10_mutant_annotation.tsv
Peak caller: MACS2
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total | 285734809 | 230000645 | 345095073 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 285734809 | 230000645 | 345095073 |
| Mapped(QC-failed) | 0 | 0 | 0 |
| % Mapped | 100.0000 | 100.0000 | 100.0000 |
| Paired | 0 | 0 | 0 |
| Paired(QC-failed) | 0 | 0 | 0 |
| Read1 | 0 | 0 | 0 |
| Read1(QC-failed) | 0 | 0 | 0 |
| Read2 | 0 | 0 | 0 |
| Read2(QC-failed) | 0 | 0 | 0 |
| Properly Paired | 0 | 0 | 0 |
| Properly Paired(QC-failed) | 0 | 0 | 0 |
| % Properly Paired | 0.0000 | 0.0000 | 0.0000 |
| With itself | 0 | 0 | 0 |
| With itself(QC-failed) | 0 | 0 | 0 |
| Singletons | 0 | 0 | 0 |
| Singletons(QC-failed) | 0 | 0 | 0 |
| % Singleton | 0.0000 | 0.0000 | 0.0000 |
| Diff. Chroms | 0 | 0 | 0 |
| Diff. Chroms (QC-failed) | 0 | 0 | 0 |
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total Reads | 285730536 | 229996803 | 345077892 |
| Distinct Reads | 137715090 | 106198054 | 151425175 |
| One Read | None | None | None |
| Two Reads | None | None | None |
| NRF = Distinct/Total | 0.4820 | 0.4617 | 0.4388 |
| PBC1 = OneRead/Distinct | None | None | None |
| PBC2 = OneRead/TwoReads | None | None | None |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
Filtered and duplicates removed
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total | 137717502 | 106200119 | 151433576 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 137717502 | 106200119 | 151433576 |
| Mapped(QC-failed) | 0 | 0 | 0 |
| % Mapped | 100.0000 | 100.0000 | 100.0000 |
| Paired | 0 | 0 | 0 |
| Paired(QC-failed) | 0 | 0 | 0 |
| Read1 | 0 | 0 | 0 |
| Read1(QC-failed) | 0 | 0 | 0 |
| Read2 | 0 | 0 | 0 |
| Read2(QC-failed) | 0 | 0 | 0 |
| Properly Paired | 0 | 0 | 0 |
| Properly Paired(QC-failed) | 0 | 0 | 0 |
| % Properly Paired | 0.0000 | 0.0000 | 0.0000 |
| With itself | 0 | 0 | 0 |
| With itself(QC-failed) | 0 | 0 | 0 |
| Singletons | 0 | 0 | 0 |
| Singletons(QC-failed) | 0 | 0 | 0 |
| % Singleton | 0.0000 | 0.0000 | 0.0000 |
| Diff. Chroms | 0 | 0 | 0 |
| Diff. Chroms (QC-failed) | 0 | 0 | 0 |
The number of peaks is capped at 500K for peak-caller MACS2
| overlap | IDR | |
|---|---|---|
| Nt | 211753 | 135483 |
| N1 | 175215 | 96389 |
| N2 | 167226 | 13055 |
| N3 | 191744 | 24649 |
| Np | 228004 | 89445 |
| N optimal | 228004 | 135483 |
| N conservative | 211753 | 135483 |
| Optimal Set | ppr | rep1-rep3 |
| Conservative Set | rep1-rep3 | rep1-rep3 |
| Rescue Ratio | 1.0767 | 1.5147 |
| Self Consistency Ratio | 1.1466 | 7.3833 |
| Reproducibility | pass | borderline |
Overlapping peaks
IDR (Irreproducible Discovery Rate) peaks
| rep1-rep2 | rep1-rep3 | rep2-rep3 | rep1-pr | rep2-pr | rep3-pr | ppr | |
|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.5587 | 0.5634 | 0.5601 | 0.5532 | 0.5628 | 0.5240 | 0.5693 |
| rep1-rep2 | rep1-rep3 | rep2-rep3 | rep1-pr | rep2-pr | rep3-pr | ppr | |
|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.5161 | 0.5267 | 0.5193 | 0.5023 | 0.3115 | 0.3314 | 0.4897 |