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Report generated at 2020-07-10 08:14:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	64974182	104183442
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60821438	101561725
Mapped(QC-failed)	0	0
% Mapped	93.6100	97.4800
Paired	64974182	104183442
Paired(QC-failed)	0	0
Read1	32487091	52091721
Read1(QC-failed)	0	0
Read2	32487091	52091721
Read2(QC-failed)	0	0
Properly Paired	59307955	83193856
Properly Paired(QC-failed)	0	0
% Properly Paired	91.2800	79.8500
With itself	60361709	100020683
With itself(QC-failed)	0	0
Singletons	459729	1541042
Singletons(QC-failed)	0	0
% Singleton	0.7100	1.4800
Diff. Chroms	545825	13877524
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	26820179	36259719
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12471611	570314
Paired Opt. Dupes	1429	2544
% Dupes/100	0.4650	0.0157

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26803860	36250789
Distinct Read Pairs	14340268	35680935
One Read Pair	7022256	35127299
Two Read Pairs	4134135	542681
NRF = Distinct/Total	0.5350	0.9843
PBC1 = OnePair/Distinct	0.4897	0.9845
PBC2 = OnePair/TwoPair	1.6986	64.7292

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	28697136	71378810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28697136	71378810
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	28697136	71378810
Paired(QC-failed)	0	0
Read1	14348568	35689405
Read1(QC-failed)	0	0
Read2	14348568	35689405
Read2(QC-failed)	0	0
Properly Paired	28697136	71378810
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	28697136	71378810
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	112356
Np	0
N optimal	112356
N conservative	112356
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.	150
Corr. Est. Fragment Len.	0.1892
Phantom Peak	55
Corr. Phantom Peak	0.1379
Argmin. Corr.	1500
Min. Corr.	0.1138
NSC	1.6629
RSC	3.1332

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	0.3255

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	0.1367
AUC	0.4924
CHANCE divergence	0.3817
Elbow Point	0.0000
JS Distance	0.6974
Synthetic AUC	0.5024
Synthetic Elbow Point	0.2953
Synthetic JS Distance	0.4286