chipnexus data from julias lab
Pipeline version: v1.1.6
Report generated at 2020-02-20 09:03:35
Paired-end: False
Pipeline type: ChIP-nexus
Genome: mm10_sox2crispr1_mutant_annotation.tsv
Peak caller: MACS2
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total | 213046217 | 194315905 | 230595069 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 213046217 | 194315905 | 230595069 |
| 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 | 213025150 | 194292846 | 230560508 |
| Distinct Reads | 122060072 | 122855458 | 119928463 |
| One Read | None | None | None |
| Two Reads | None | None | None |
| NRF = Distinct/Total | 0.5730 | 0.6323 | 0.5202 |
| 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 | 122073355 | 122871190 | 119947637 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 122073355 | 122871190 | 119947637 |
| 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 | 139482 | 73393 |
| N1 | 105288 | 47379 |
| N2 | 104034 | 46026 |
| N3 | 98364 | 45156 |
| Np | 167498 | 93352 |
| N optimal | 167498 | 93352 |
| N conservative | 139482 | 73393 |
| Optimal Set | ppr | ppr |
| Conservative Set | rep1-rep2 | rep1-rep2 |
| Rescue Ratio | 1.2009 | 1.2719 |
| Self Consistency Ratio | 1.0704 | 1.0492 |
| 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 | 0.1956 | 0.1922 | 0.1917 | 0.1692 | 0.1640 | 0.1729 | 0.2066 |
| rep1-rep2 | rep1-rep3 | rep2-rep3 | rep1-pr | rep2-pr | rep3-pr | ppr | |
|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.1572 | 0.1541 | 0.1523 | 0.1276 | 0.1233 | 0.1331 | 0.1709 |