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Report generated at 2021-02-05 15:54:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52410916	114808036
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51810722	112966653
Mapped(QC-failed)	0	0
% Mapped	98.8500	98.4000
Paired	52410916	114808036
Paired(QC-failed)	0	0
Read1	26205458	57404018
Read1(QC-failed)	0	0
Read2	26205458	57404018
Read2(QC-failed)	0	0
Properly Paired	51310957	111166608
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9000	96.8300
With itself	51541189	112278723
With itself(QC-failed)	0	0
Singletons	269533	687930
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.6000
Diff. Chroms	30757	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	23135875	48311888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	203339	307480
Paired Opt. Dupes	39379	76418
% Dupes/100	0.0088	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23090138	48289765
Distinct Read Pairs	22889406	47983591
One Read Pair	22691996	47690244
Two Read Pairs	194359	287957
NRF = Distinct/Total	0.9913	0.9937
PBC1 = OnePair/Distinct	0.9914	0.9939
PBC2 = OnePair/TwoPair	116.7530	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	45865072	96008816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45865072	96008816
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45865072	96008816
Paired(QC-failed)	0	0
Read1	22932536	48004408
Read1(QC-failed)	0	0
Read2	22932536	48004408
Read2(QC-failed)	0	0
Properly Paired	45865072	96008816
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45865072	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	77766
Np	0
N optimal	77766
N conservative	77766
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.	150
Corr. Est. Fragment Len.	0.1855
Phantom Peak	50
Corr. Phantom Peak	0.1796
Argmin. Corr.	1500
Min. Corr.	0.1673
NSC	1.1085
RSC	1.4732

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	0.2000

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	0.2451
AUC	0.4938
CHANCE divergence	0.1278
Elbow Point	0.0000
JS Distance	0.6505
Synthetic AUC	0.5079
Synthetic Elbow Point	0.1926
Synthetic JS Distance	0.3369