chipnexus data from julias lab
Pipeline version: v1.1.6
Report generated at 2020-02-20 19:26:24
Paired-end: False
Pipeline type: ChIP-nexus
Genome: mm10_sox2crispr1_mutant_annotation.tsv
Peak caller: MACS2
| rep1 | rep2 | rep3 | |
|---|---|---|---|
| Total | 251068216 | 206108730 | 311704016 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 251068216 | 206108730 | 311704016 |
| 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 | 251061827 | 206103029 | 311693270 |
| Distinct Reads | 138467256 | 146785236 | 167580780 |
| One Read | None | None | None |
| Two Reads | None | None | None |
| NRF = Distinct/Total | 0.5515 | 0.7122 | 0.5376 |
| 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 | 138471343 | 146789710 | 167587350 |
| Total(QC-failed) | 0 | 0 | 0 |
| Dupes | 0 | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 | 0 |
| Mapped | 138471343 | 146789710 | 167587350 |
| 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 | 194709 | 124143 |
| N1 | 166923 | 16798 |
| N2 | 172785 | 68921 |
| N3 | 174903 | 11643 |
| Np | 214856 | 37831 |
| N optimal | 214856 | 124143 |
| N conservative | 194709 | 124143 |
| Optimal Set | ppr | rep1-rep2 |
| Conservative Set | rep1-rep2 | rep1-rep2 |
| Rescue Ratio | 1.1035 | 3.2815 |
| Self Consistency Ratio | 1.0478 | 5.9195 |
| Reproducibility | pass | fail |
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 | 0.5223 | 0.5200 | 0.5205 | 0.5172 | 0.4755 | 0.5229 | 0.5298 |
| rep1-rep2 | rep1-rep3 | rep2-rep3 | rep1-pr | rep2-pr | rep3-pr | ppr | |
|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.4870 | 0.4833 | 0.4820 | 0.3095 | 0.4018 | 0.2816 | 0.3791 |