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Report generated at 2019-12-03 10:16:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	59906888	96981564
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55296250	94057636
Mapped(QC-failed)	0	0
% Mapped	92.3000	96.9900
Paired	59906888	96981564
Paired(QC-failed)	0	0
Read1	29953444	48490782
Read1(QC-failed)	0	0
Read2	29953444	48490782
Read2(QC-failed)	0	0
Properly Paired	54236795	90998199
Properly Paired(QC-failed)	0	0
% Properly Paired	90.5400	93.8300
With itself	54672869	93287611
With itself(QC-failed)	0	0
Singletons	623381	770025
Singletons(QC-failed)	0	0
% Singleton	1.0400	0.7900
Diff. Chroms	86464	205681
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	24046830	40192164
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12344171	554748
Paired Opt. Dupes	8366	11605
% Dupes/100	0.5133	0.0138

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24046615	40177379
Distinct Read Pairs	11702540	39622917
One Read Pair	6462498	39079490
Two Read Pairs	2428612	534171
NRF = Distinct/Total	0.4867	0.9862
PBC1 = OnePair/Distinct	0.5522	0.9863
PBC2 = OnePair/TwoPair	2.6610	73.1591

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	23405318	79274832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	23405318	79274832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	23405318	79274832
Paired(QC-failed)	0	0
Read1	11702659	39637416
Read1(QC-failed)	0	0
Read2	11702659	39637416
Read2(QC-failed)	0	0
Properly Paired	23405318	79274832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	23405318	79274832
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	91085
Np	0
N optimal	91085
N conservative	91085
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.	105
Corr. Est. Fragment Len.	0.1256
Phantom Peak	50
Corr. Phantom Peak	0.1120
Argmin. Corr.	1500
Min. Corr.	0.0994
NSC	1.2632
RSC	2.0840

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	0.1374

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	0.1953
AUC	0.4916
CHANCE divergence	0.2997
Elbow Point	0.0000
JS Distance	0.6137
Synthetic AUC	0.4935
Synthetic Elbow Point	0.1749
Synthetic JS Distance	0.3213