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Report generated at 2019-10-25 12:13:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	99517960	127273172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98372190	125877623
Mapped(QC-failed)	0	0
% Mapped	98.8500	98.9000
Paired	99517960	127273172
Paired(QC-failed)	0	0
Read1	49758980	63636586
Read1(QC-failed)	0	0
Read2	49758980	63636586
Read2(QC-failed)	0	0
Properly Paired	96601007	121731620
Properly Paired(QC-failed)	0	0
% Properly Paired	97.0700	95.6500
With itself	97847932	125137848
With itself(QC-failed)	0	0
Singletons	524258	739775
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.5800
Diff. Chroms	798092	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	41247475	50825445
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2956154	3188108
Paired Opt. Dupes	9368	6482
% Dupes/100	0.0717	0.0627

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41246729	50816662
Distinct Read Pairs	38290617	47629109
One Read Pair	35483921	44580671
Two Read Pairs	2665134	2916506
NRF = Distinct/Total	0.9283	0.9373
PBC1 = OnePair/Distinct	0.9267	0.9360
PBC2 = OnePair/TwoPair	13.3141	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	76582642	95274674
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76582642	95274674
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76582642	95274674
Paired(QC-failed)	0	0
Read1	38291321	47637337
Read1(QC-failed)	0	0
Read2	38291321	47637337
Read2(QC-failed)	0	0
Properly Paired	76582642	95274674
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76582642	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	122612
Np	0
N optimal	122612
N conservative	122612
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.	0.1790
Phantom Peak	50
Corr. Phantom Peak	0.1899
Argmin. Corr.	1500
Min. Corr.	0.1721
NSC	1.0400
RSC	0.3869

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	0.2484

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	0.2571
AUC	0.4943
CHANCE divergence	0.1113
Elbow Point	0.0000
JS Distance	0.6713
Synthetic AUC	0.5100
Synthetic Elbow Point	0.1954
Synthetic JS Distance	0.3179