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Report generated at 2019-10-26 04:01:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	204221064	127273172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	200441466	125877623
Mapped(QC-failed)	0	0
% Mapped	98.1500	98.9000
Paired	204221064	127273172
Paired(QC-failed)	0	0
Read1	102110532	63636586
Read1(QC-failed)	0	0
Read2	102110532	63636586
Read2(QC-failed)	0	0
Properly Paired	195163581	121731620
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5600	95.6500
With itself	198668665	125137848
With itself(QC-failed)	0	0
Singletons	1772801	739775
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.5800
Diff. Chroms	2341345	1957878
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	81293729	50825445
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11792821	3188108
Paired Opt. Dupes	21038	6482
% Dupes/100	0.1451	0.0627

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	81292796	50816662
Distinct Read Pairs	69500112	47629109
One Read Pair	59154105	44580671
Two Read Pairs	9058914	2916506
NRF = Distinct/Total	0.8549	0.9373
PBC1 = OnePair/Distinct	0.8511	0.9360
PBC2 = OnePair/TwoPair	6.5299	15.2856

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	139001816	95274674
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139001816	95274674
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	139001816	95274674
Paired(QC-failed)	0	0
Read1	69500908	47637337
Read1(QC-failed)	0	0
Read2	69500908	47637337
Read2(QC-failed)	0	0
Properly Paired	139001816	95274674
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	139001816	95274674
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	129150
Np	0
N optimal	129150
N conservative	129150
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.	125
Corr. Est. Fragment Len.	0.1773
Phantom Peak	50
Corr. Phantom Peak	0.1860
Argmin. Corr.	1500
Min. Corr.	0.1734
NSC	1.0227
RSC	0.3118

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	0.1188

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	0.2812
AUC	0.4958
CHANCE divergence	0.1018
Elbow Point	0.0000
JS Distance	0.5731
Synthetic AUC	0.5042
Synthetic Elbow Point	0.1282
Synthetic JS Distance	0.2814