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Report generated at 2019-10-13 01:43:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	109464264	95805330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103012387	91174239
Mapped(QC-failed)	0	0
% Mapped	94.1100	95.1700
Paired	109464264	95805330
Paired(QC-failed)	0	0
Read1	54732132	47902665
Read1(QC-failed)	0	0
Read2	54732132	47902665
Read2(QC-failed)	0	0
Properly Paired	98802106	87029614
Properly Paired(QC-failed)	0	0
% Properly Paired	90.2600	90.8400
With itself	99509330	88132031
With itself(QC-failed)	0	0
Singletons	3503057	3042208
Singletons(QC-failed)	0	0
% Singleton	3.2000	3.1800
Diff. Chroms	320190	677774
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	41215083	36289675
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13010981	346498
Paired Opt. Dupes	4872	3852
% Dupes/100	0.3157	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41214112	36261516
Distinct Read Pairs	28203410	35915541
One Read Pair	19430578	35581631
Two Read Pairs	5932858	326616
NRF = Distinct/Total	0.6843	0.9905
PBC1 = OnePair/Distinct	0.6889	0.9907
PBC2 = OnePair/TwoPair	3.2751	108.9403

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	56408204	71886354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56408204	71886354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56408204	71886354
Paired(QC-failed)	0	0
Read1	28204102	35943177
Read1(QC-failed)	0	0
Read2	28204102	35943177
Read2(QC-failed)	0	0
Properly Paired	56408204	71886354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56408204	71886354
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	38736
Np	0
N optimal	38736
N conservative	38736
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.	0.1532
Phantom Peak	50
Corr. Phantom Peak	0.1607
Argmin. Corr.	1500
Min. Corr.	0.1480
NSC	1.0350
RSC	0.4073

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	0.0289

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	0.3064
AUC	0.4946
CHANCE divergence	0.1063
Elbow Point	0.0000
JS Distance	0.5387
Synthetic AUC	0.5035
Synthetic Elbow Point	0.0468
Synthetic JS Distance	0.2310