chipnexus data from julias lab
Pipeline version: v1.1.6
Report generated at 2020-03-23 20:00:35
Paired-end: False
Pipeline type: ChIP-nexus
Genome: mm10_mutant_annotation.tsv
Peak caller: MACS2
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total | 193629728 | 189950470 | 257263393 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 193629728 | 189950470 | 257263393 |
| 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 | 193604402 | 189923163 | 257189806 |
| Distinct Reads | 85074201 | 100162662 | 118872840 |
| One Read | None | None | None |
| Two Reads | None | None | None |
| NRF = Distinct/Total | 0.4394 | 0.5274 | 0.4622 |
| 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 | 85087167 | 100179162 | 118909493 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 85087167 | 100179162 | 118909493 |
| 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 | 151318 | 79977 |
| N1 | 104428 | 44149 |
| N2 | 125864 | 59005 |
| N3 | 115643 | 52844 |
| Np | 168146 | 95658 |
| N optimal | 168146 | 95658 |
| N conservative | 151318 | 79977 |
| Optimal Set | ppr | ppr |
| Conservative Set | rep2-rep3 | rep2-rep3 |
| Rescue Ratio | 1.1112 | 1.1961 |
| Self Consistency Ratio | 1.2053 | 1.3365 |
| Reproducibility | pass | pass |
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 | 0.2178 | 0.2165 | 0.2235 | 0.1831 | 0.2266 | 0.1813 | 0.2304 |
| rep1-rep2 | rep1-rep3 | rep2-rep3 | rep1-pr | rep2-pr | rep3-pr | ppr | |
|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.1753 | 0.1736 | 0.1825 | 0.1386 | 0.1791 | 0.1391 | 0.1934 |