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Report generated at 2020-06-05 15:55:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	83414522	74925678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76399105	73334040
Mapped(QC-failed)	0	0
% Mapped	91.5900	97.8800
Paired	83414522	74925678
Paired(QC-failed)	0	0
Read1	41707261	37462839
Read1(QC-failed)	0	0
Read2	41707261	37462839
Read2(QC-failed)	0	0
Properly Paired	75538908	72502624
Properly Paired(QC-failed)	0	0
% Properly Paired	90.5600	96.7700
With itself	76061317	73039911
With itself(QC-failed)	0	0
Singletons	337788	294129
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.3900
Diff. Chroms	57323	216939
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	34163271	32127407
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12444706	360854
Paired Opt. Dupes	2504	4136
% Dupes/100	0.3643	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34157943	31804933
Distinct Read Pairs	21715236	31477794
One Read Pair	13286892	31163507
Two Read Pairs	5597089	307462
NRF = Distinct/Total	0.6357	0.9897
PBC1 = OnePair/Distinct	0.6119	0.9900
PBC2 = OnePair/TwoPair	2.3739	101.3573

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	43437130	63533106
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43437130	63533106
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43437130	63533106
Paired(QC-failed)	0	0
Read1	21718565	31766553
Read1(QC-failed)	0	0
Read2	21718565	31766553
Read2(QC-failed)	0	0
Properly Paired	43437130	63533106
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43437130	63533106
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	56626
Np	0
N optimal	56626
N conservative	56626
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.	0.2251
Phantom Peak	50
Corr. Phantom Peak	0.2118
Argmin. Corr.	1500
Min. Corr.	0.1526
NSC	1.4754
RSC	1.2261

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	0.3280

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	0.1986
AUC	0.4938
CHANCE divergence	0.1465
Elbow Point	0.0000
JS Distance	0.7383
Synthetic AUC	0.4985
Synthetic Elbow Point	0.3338
Synthetic JS Distance	0.4327