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Report generated at 2019-10-13 00:37:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106455232	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89176301	86768459
Mapped(QC-failed)	0	0
% Mapped	83.7700	97.7100
Paired	106455232	88801120
Paired(QC-failed)	0	0
Read1	53227616	44400560
Read1(QC-failed)	0	0
Read2	53227616	44400560
Read2(QC-failed)	0	0
Properly Paired	88337209	85806359
Properly Paired(QC-failed)	0	0
% Properly Paired	82.9800	96.6300
With itself	88769630	86430737
With itself(QC-failed)	0	0
Singletons	406671	337722
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.3800
Diff. Chroms	93868	102712
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	38216842	37886939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2110636	723026
Paired Opt. Dupes	3344	3740
% Dupes/100	0.0552	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38214333	37657060
Distinct Read Pairs	36103821	36953214
One Read Pair	34094571	36265585
Two Read Pairs	1912563	673617
NRF = Distinct/Total	0.9448	0.9813
PBC1 = OnePair/Distinct	0.9443	0.9814
PBC2 = OnePair/TwoPair	17.8266	53.8371

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	72212412	74327826
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72212412	74327826
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72212412	74327826
Paired(QC-failed)	0	0
Read1	36106206	37163913
Read1(QC-failed)	0	0
Read2	36106206	37163913
Read2(QC-failed)	0	0
Properly Paired	72212412	74327826
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72212412	74327826
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	52620
Np	0
N optimal	52620
N conservative	52620
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.	0.1744
Phantom Peak	50
Corr. Phantom Peak	0.1875
Argmin. Corr.	1500
Min. Corr.	0.1707
NSC	1.0218
RSC	0.2218

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	0.0210

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	0.3165
AUC	0.4952
CHANCE divergence	0.1018
Elbow Point	0.0000
JS Distance	0.5124
Synthetic AUC	0.5089
Synthetic Elbow Point	0.0519
Synthetic JS Distance	0.2206