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Report generated at 2020-06-08 07:55:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	302586222	103045968
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	295185401	98644908
Mapped(QC-failed)	0	0
% Mapped	97.5500	95.7300
Paired	302586222	103045968
Paired(QC-failed)	0	0
Read1	151293111	51522984
Read1(QC-failed)	0	0
Read2	151293111	51522984
Read2(QC-failed)	0	0
Properly Paired	289173143	94442886
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5700	91.6500
With itself	290573346	95330195
With itself(QC-failed)	0	0
Singletons	4612055	3314713
Singletons(QC-failed)	0	0
% Singleton	1.5200	3.2200
Diff. Chroms	634833	525331
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	126673220	40142877
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14918456	1418251
Paired Opt. Dupes	16465	4354
% Dupes/100	0.1178	0.0353

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	126671012	40111338
Distinct Read Pairs	111752812	38694462
One Read Pair	98394314	37332587
Two Read Pairs	11950140	1311871
NRF = Distinct/Total	0.8822	0.9647
PBC1 = OnePair/Distinct	0.8805	0.9648
PBC2 = OnePair/TwoPair	8.2337	28.4575

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	223509528	77449252
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	223509528	77449252
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	223509528	77449252
Paired(QC-failed)	0	0
Read1	111754764	38724626
Read1(QC-failed)	0	0
Read2	111754764	38724626
Read2(QC-failed)	0	0
Properly Paired	223509528	77449252
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	223509528	77449252
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

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	138643
Np	0
N optimal	138643
N conservative	138643
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

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

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	140
Corr. Est. Fragment Len.	0.1765
Phantom Peak	50
Corr. Phantom Peak	0.1834
Argmin. Corr.	1500
Min. Corr.	0.1716
NSC	1.0289
RSC	0.4199

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

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

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.1968

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)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2945
AUC	0.4973
CHANCE divergence	0.0965
Elbow Point	0.0000
JS Distance	0.6768
Synthetic AUC	0.5006
Synthetic Elbow Point	0.1416
Synthetic JS Distance	0.2744