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Report generated at 2021-03-18 16:22:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	29850892	141252688
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	29096300	137128851
Mapped(QC-failed)	0	0
% Mapped	97.4700	97.0800
Paired	29850892	141252688
Paired(QC-failed)	0	0
Read1	14925446	70626344
Read1(QC-failed)	0	0
Read2	14925446	70626344
Read2(QC-failed)	0	0
Properly Paired	27480759	120202392
Properly Paired(QC-failed)	0	0
% Properly Paired	92.0600	85.1000
With itself	28934600	135538631
With itself(QC-failed)	0	0
Singletons	161700	1590220
Singletons(QC-failed)	0	0
% Singleton	0.5400	1.1300
Diff. Chroms	1048288	10787220
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	12522078	53575957
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	183574	637468
Paired Opt. Dupes	3338	1319
% Dupes/100	0.0147	0.0119

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	12512562	53569792
Distinct Read Pairs	12329469	52932780
One Read Pair	12161662	52328435
Two Read Pairs	157035	584956
NRF = Distinct/Total	0.9854	0.9881
PBC1 = OnePair/Distinct	0.9864	0.9886
PBC2 = OnePair/TwoPair	77.4455	89.4570

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	24677008	105876978
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24677008	105876978
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24677008	105876978
Paired(QC-failed)	0	0
Read1	12338504	52938489
Read1(QC-failed)	0	0
Read2	12338504	52938489
Read2(QC-failed)	0	0
Properly Paired	24677008	105876978
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24677008	105876978
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	94516
Np	0
N optimal	94516
N conservative	94516
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 (14M)

	rep1
Reads	14637557
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.2272
Phantom Peak	55
Corr. Phantom Peak	0.1935
Argmin. Corr.	1500
Min. Corr.	0.1620
NSC	1.4024
RSC	2.0725

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	0.4548

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	0.1252
AUC	0.4918
CHANCE divergence	0.3209
Elbow Point	0.0000
JS Distance	0.7687
Synthetic AUC	0.5110
Synthetic Elbow Point	0.3850
Synthetic JS Distance	0.4893