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Report generated at 2020-05-03 17:44:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	105608280	75348014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94567857	72639776
Mapped(QC-failed)	0	0
% Mapped	89.5500	96.4100
Paired	105608280	75348014
Paired(QC-failed)	0	0
Read1	52804140	37674007
Read1(QC-failed)	0	0
Read2	52804140	37674007
Read2(QC-failed)	0	0
Properly Paired	91614312	70114889
Properly Paired(QC-failed)	0	0
% Properly Paired	86.7500	93.0500
With itself	93223896	71857749
With itself(QC-failed)	0	0
Singletons	1343961	782027
Singletons(QC-failed)	0	0
% Singleton	1.2700	1.0400
Diff. Chroms	484452	1077494
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	33317631	30082479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	208165	117823
Paired Opt. Dupes	1222	447
% Dupes/100	0.0062	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33315044	30056490
Distinct Read Pairs	33106899	29938925
One Read Pair	32908249	29821774
Two Read Pairs	191394	116742
NRF = Distinct/Total	0.9938	0.9961
PBC1 = OnePair/Distinct	0.9940	0.9961
PBC2 = OnePair/TwoPair	171.9398	255.4503

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	66218932	59929312
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66218932	59929312
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66218932	59929312
Paired(QC-failed)	0	0
Read1	33109466	29964656
Read1(QC-failed)	0	0
Read2	33109466	29964656
Read2(QC-failed)	0	0
Properly Paired	66218932	59929312
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66218932	59929312
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	169984
Np	0
N optimal	169984
N conservative	169984
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.	130
Corr. Est. Fragment Len.	0.2101
Phantom Peak	50
Corr. Phantom Peak	0.2616
Argmin. Corr.	1500
Min. Corr.	0.1945
NSC	1.0801
RSC	0.2319

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	0.1532

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	0.2506
AUC	0.4950
CHANCE divergence	0.1069
Elbow Point	0.0000
JS Distance	0.6416
Synthetic AUC	0.5071
Synthetic Elbow Point	0.0746
Synthetic JS Distance	0.3270