chipnexus data from julias lab - wt.Sox2
Pipeline version: v1.1.6
Report generated at 2020-02-19 10:01:02
Paired-end: False
Pipeline type: ChIP-nexus
Genome: mm10_sherlock.tsv
Peak caller: MACS2
| rep1 | rep2 | |
|---|---|---|
| Total | 172068682 | 198240035 |
| Total(QC-failed) | 0 | 0 |
| Dupes | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 |
| Mapped | 172068682 | 198240035 |
| Mapped(QC-failed) | 0 | 0 |
| % Mapped | 100.0000 | 100.0000 |
| Paired | 0 | 0 |
| Paired(QC-failed) | 0 | 0 |
| Read1 | 0 | 0 |
| Read1(QC-failed) | 0 | 0 |
| Read2 | 0 | 0 |
| Read2(QC-failed) | 0 | 0 |
| Properly Paired | 0 | 0 |
| Properly Paired(QC-failed) | 0 | 0 |
| % Properly Paired | 0.0000 | 0.0000 |
| With itself | 0 | 0 |
| With itself(QC-failed) | 0 | 0 |
| Singletons | 0 | 0 |
| Singletons(QC-failed) | 0 | 0 |
| % Singleton | 0.0000 | 0.0000 |
| Diff. Chroms | 0 | 0 |
| Diff. Chroms (QC-failed) | 0 | 0 |
| rep1 | rep2 | |
|---|---|---|
| Total Reads | 172051409 | 198224829 |
| Distinct Reads | 101205995 | 96346535 |
| One Read | None | None |
| Two Reads | None | None |
| NRF = Distinct/Total | 0.5882 | 0.4860 |
| PBC1 = OneRead/Distinct | None | None |
| PBC2 = OneRead/TwoReads | 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 | |
|---|---|---|
| Total | 101217199 | 96355001 |
| Total(QC-failed) | 0 | 0 |
| Dupes | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 |
| Mapped | 101217199 | 96355001 |
| Mapped(QC-failed) | 0 | 0 |
| % Mapped | 100.0000 | 100.0000 |
| Paired | 0 | 0 |
| Paired(QC-failed) | 0 | 0 |
| Read1 | 0 | 0 |
| Read1(QC-failed) | 0 | 0 |
| Read2 | 0 | 0 |
| Read2(QC-failed) | 0 | 0 |
| Properly Paired | 0 | 0 |
| Properly Paired(QC-failed) | 0 | 0 |
| % Properly Paired | 0.0000 | 0.0000 |
| With itself | 0 | 0 |
| With itself(QC-failed) | 0 | 0 |
| Singletons | 0 | 0 |
| Singletons(QC-failed) | 0 | 0 |
| % Singleton | 0.0000 | 0.0000 |
| Diff. Chroms | 0 | 0 |
| Diff. Chroms (QC-failed) | 0 | 0 |
The number of peaks is capped at 500K for peak-caller MACS2
| overlap | IDR | |
|---|---|---|
| Nt | 133387 | 67574 |
| N1 | 106405 | 46858 |
| N2 | 104195 | 46439 |
| Np | 136157 | 69414 |
| N optimal | 136157 | 69414 |
| N conservative | 133387 | 67574 |
| Optimal Set | ppr | ppr |
| Conservative Set | rep1-rep2 | rep1-rep2 |
| Rescue Ratio | 1.0208 | 1.0272 |
| Self Consistency Ratio | 1.0212 | 1.0090 |
| Reproducibility | pass | pass |
Overlapping peaks
IDR (Irreproducible Discovery Rate) peaks
| rep1-rep2 | rep1-pr | rep2-pr | ppr | |
|---|---|---|---|---|
| Fraction of Reads in Peak | 0.1984 | 0.1704 | 0.1872 | 0.1996 |
| rep1-rep2 | rep1-pr | rep2-pr | ppr | |
|---|---|---|---|---|
| Fraction of Reads in Peak | 0.1585 | 0.1283 | 0.1433 | 0.1599 |