Enrichment QC (strand cross-correlation measures)
| Reads | 15000000 |
|---|---|
| Est. Fragment Len. | -5 |
| Corr. Est. Fragment Len. | 0.208450987415934 |
| Phantom Peak | 65 |
| Corr. Phantom Peak | 0.2202027 |
| Argmin. Corr. | 1500 |
| Min. Corr. | 0.1856339 |
| NSC | 1.122914 |
| RSC | 0.6600478 |
NOTE: Reads from replicates are subsampled to a max of 15M
- Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
- Relative strand cross-correlation coefficient (RSC) = col10 in outFile
- Estimated fragment length = col3 in outFile, take the top value
Number of peaks
| rep1 | 70692 |
|---|---|
| rep1-pr1 | 68829 |
| rep1-pr2 | 68441 |
- ppr1: Raw peaks called on the first pooled pseudoreplicates
- ppr2: Raw peaks called on the second pooled pseudoreplicates
- repi: Raw peaks called on true replicate i
- repi-pr1 : Raw peaks called on the first pseudoreplicate from replicate i
- repi-pr2 : Raw peaks called on the second pseudoreplicates from replicate i
- overlap : Overlapped peaks (filtered if blacklist exists)
Enrichment QC (Fraction of reads in raw peaks)
| Fraction of Reads in Peak | 0.0886069 |
|---|
Enrichment QC (Fraction of reads in overlapping peaks)
| Fraction of Reads in Peak | 0.0748033 |
|---|
- ppr: Overlapping peaks comparing pooled pseudo replicates
- rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
- rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
- repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)
Reproducibility QC and Peak Detection Statistics (Overlapping peaks)
| Nt | 0 |
|---|---|
| N1 | 36996 |
| N2 | 0 |
| Np | 0 |
| N optimal | 36996 |
| N conservative | 36996 |
| Optimal Set | self_pseudo_rep_rep1 |
| Conservative Set | self_pseudo_rep_rep1 |
| Rescue Ratio | 0.0 |
| Self Consistency Ratio | 1.0 |
| Reproducibility Test | pass |
- N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
- N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
- Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
- Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
- Self-consistency Ratio: max(N1,N2) / min (N1,N2)
- Rescue Ratio: max(Np,Nt) / min (Np,Nt)
- Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'
Enrichment QC (Fraction of reads in IDR peaks)
| Fraction of Reads in Peak | 0.0598221 |
|---|
- ppr: IDR peaks comparing pooled pseudo replicates
- rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
- rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
- repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)
Reproducibility QC and Peak Detection Statistics (Irreproducible Discovery Rate)
| Nt | 0 |
|---|---|
| N1 | 18017 |
| N2 | 0 |
| Np | 0 |
| N optimal | 18017 |
| N conservative | 18017 |
| Optimal Set | self_pseudo_rep_rep1 |
| Conservative Set | self_pseudo_rep_rep1 |
| Rescue Ratio | 0.0 |
| Self Consistency Ratio | 1.0 |
| Reproducibility Test | pass |
- N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
- N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
- Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
- Np: Pooled-pseudoreplicate consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
- Self-consistency Ratio: max(N1,N2) / min (N1,N2)
- Rescue Ratio: max(Np,Nt) / min (Np,Nt)
- Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'
