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Report generated at 2020-05-14 03:00:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	53236194	85104728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49116277	81834549
Mapped(QC-failed)	0	0
% Mapped	92.2600	96.1600
Paired	53236194	85104728
Paired(QC-failed)	0	0
Read1	26618097	42552364
Read1(QC-failed)	0	0
Read2	26618097	42552364
Read2(QC-failed)	0	0
Properly Paired	47798662	77417456
Properly Paired(QC-failed)	0	0
% Properly Paired	89.7900	90.9700
With itself	48268900	79446512
With itself(QC-failed)	0	0
Singletons	847377	2388037
Singletons(QC-failed)	0	0
% Singleton	1.5900	2.8100
Diff. Chroms	342135	1421679
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	21462095	32647563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	336504	620344
Paired Opt. Dupes	2593	1489
% Dupes/100	0.0157	0.0190

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21460904	32646807
Distinct Read Pairs	21124419	32026480
One Read Pair	20792498	31415922
Two Read Pairs	327414	600925
NRF = Distinct/Total	0.9843	0.9810
PBC1 = OnePair/Distinct	0.9843	0.9809
PBC2 = OnePair/TwoPair	63.5052	52.2793

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	42251182	64054438
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42251182	64054438
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42251182	64054438
Paired(QC-failed)	0	0
Read1	21125591	32027219
Read1(QC-failed)	0	0
Read2	21125591	32027219
Read2(QC-failed)	0	0
Properly Paired	42251182	64054438
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42251182	64054438
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	25740
Np	0
N optimal	25740
N conservative	25740
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.	260
Corr. Est. Fragment Len.	0.4086
Phantom Peak	55
Corr. Phantom Peak	0.3542
Argmin. Corr.	1500
Min. Corr.	0.1908
NSC	2.1412
RSC	1.3324

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	0.5489

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	0.0911
AUC	0.4936
CHANCE divergence	0.3706
Elbow Point	0.0000
JS Distance	0.8207
Synthetic AUC	0.4954
Synthetic Elbow Point	0.4754
Synthetic JS Distance	0.5858