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Report generated at 2020-05-21 01:55:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	139618684	172040776
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105354621	166313177
Mapped(QC-failed)	0	0
% Mapped	75.4600	96.6700
Paired	139618684	172040776
Paired(QC-failed)	0	0
Read1	69809342	86020388
Read1(QC-failed)	0	0
Read2	69809342	86020388
Read2(QC-failed)	0	0
Properly Paired	103000719	164316966
Properly Paired(QC-failed)	0	0
% Properly Paired	73.7700	95.5100
With itself	103849518	165368990
With itself(QC-failed)	0	0
Singletons	1505103	944187
Singletons(QC-failed)	0	0
% Singleton	1.0800	0.5500
Diff. Chroms	248171	377471
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	42311395	70615481
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	468347	448995
Paired Opt. Dupes	2030	1973
% Dupes/100	0.0111	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42306739	70604488
Distinct Read Pairs	41838447	70155597
One Read Pair	41378452	69710274
Two Read Pairs	452856	441873
NRF = Distinct/Total	0.9889	0.9936
PBC1 = OnePair/Distinct	0.9890	0.9937
PBC2 = OnePair/TwoPair	91.3722	157.7609

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	83686096	140332972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83686096	140332972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	83686096	140332972
Paired(QC-failed)	0	0
Read1	41843048	70166486
Read1(QC-failed)	0	0
Read2	41843048	70166486
Read2(QC-failed)	0	0
Properly Paired	83686096	140332972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	83686096	140332972
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	154450
Np	0
N optimal	154450
N conservative	154450
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.	0.1991
Phantom Peak	50
Corr. Phantom Peak	0.2399
Argmin. Corr.	1500
Min. Corr.	0.1834
NSC	1.0860
RSC	0.2788

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	0.1119

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	0.2537
AUC	0.4956
CHANCE divergence	0.1166
Elbow Point	0.0000
JS Distance	0.6079
Synthetic AUC	0.5041
Synthetic Elbow Point	0.1239
Synthetic JS Distance	0.3183