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Report generated at 2020-05-28 08:16:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	57088538	100267900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56400882	98810235
Mapped(QC-failed)	0	0
% Mapped	98.8000	98.5500
Paired	57088538	100267900
Paired(QC-failed)	0	0
Read1	28544269	50133950
Read1(QC-failed)	0	0
Read2	28544269	50133950
Read2(QC-failed)	0	0
Properly Paired	55962193	95001401
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0300	94.7500
With itself	56100976	98214055
With itself(QC-failed)	0	0
Singletons	299906	596180
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.5900
Diff. Chroms	24034	104078
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	25335499	42286684
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	571036	312962
Paired Opt. Dupes	806	1739
% Dupes/100	0.0225	0.0074

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25328892	42271898
Distinct Read Pairs	24758057	41960091
One Read Pair	24234356	41660400
Two Read Pairs	488091	294709
NRF = Distinct/Total	0.9775	0.9926
PBC1 = OnePair/Distinct	0.9788	0.9929
PBC2 = OnePair/TwoPair	49.6513	141.3611

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	49528926	83947444
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49528926	83947444
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49528926	83947444
Paired(QC-failed)	0	0
Read1	24764463	41973722
Read1(QC-failed)	0	0
Read2	24764463	41973722
Read2(QC-failed)	0	0
Properly Paired	49528926	83947444
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49528926	83947444
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	77402
Np	0
N optimal	77402
N conservative	77402
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.	160
Corr. Est. Fragment Len.	0.2378
Phantom Peak	45
Corr. Phantom Peak	0.1928
Argmin. Corr.	1500
Min. Corr.	0.1700
NSC	1.3983
RSC	2.9821

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	0.5225

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	0.1374
AUC	0.4942
CHANCE divergence	0.1695
Elbow Point	0.0000
JS Distance	0.8407
Synthetic AUC	0.5007
Synthetic Elbow Point	0.4377
Synthetic JS Distance	0.5310