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Report generated at 2021-02-05 20:26:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108701128	114808036
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107298898	112966653
Mapped(QC-failed)	0	0
% Mapped	98.7100	98.4000
Paired	108701128	114808036
Paired(QC-failed)	0	0
Read1	54350564	57404018
Read1(QC-failed)	0	0
Read2	54350564	57404018
Read2(QC-failed)	0	0
Properly Paired	106196417	111166608
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7000	96.8300
With itself	106681151	112278723
With itself(QC-failed)	0	0
Singletons	617747	687930
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.6000
Diff. Chroms	66094	128846
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	46415760	48311888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	487903	307480
Paired Opt. Dupes	79940	76418
% Dupes/100	0.0105	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46365319	48289765
Distinct Read Pairs	45881488	47983591
One Read Pair	45404603	47690244
Two Read Pairs	471135	287957
NRF = Distinct/Total	0.9896	0.9937
PBC1 = OnePair/Distinct	0.9896	0.9939
PBC2 = OnePair/TwoPair	96.3728	165.6159

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	91855714	96008816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91855714	96008816
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91855714	96008816
Paired(QC-failed)	0	0
Read1	45927857	48004408
Read1(QC-failed)	0	0
Read2	45927857	48004408
Read2(QC-failed)	0	0
Properly Paired	91855714	96008816
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91855714	96008816
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	71272
Np	0
N optimal	71272
N conservative	71272
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.	115
Corr. Est. Fragment Len.	0.1730
Phantom Peak	50
Corr. Phantom Peak	0.1784
Argmin. Corr.	1500
Min. Corr.	0.1679
NSC	1.0300
RSC	0.4811

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	0.0416

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	0.3220
AUC	0.4956
CHANCE divergence	0.1014
Elbow Point	0.0000
JS Distance	0.5310
Synthetic AUC	0.5078
Synthetic Elbow Point	0.0416
Synthetic JS Distance	0.2104