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Report generated at 2022-09-03 09:23:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	190818724	118558004
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	182750529	117304851
Mapped(QC-failed)	0	0
% Mapped	95.7700	98.9400
Paired	190818724	118558004
Paired(QC-failed)	0	0
Read1	95409362	59279002
Read1(QC-failed)	0	0
Read2	95409362	59279002
Read2(QC-failed)	0	0
Properly Paired	179795225	116629865
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2200	98.3700
With itself	181019784	117061444
With itself(QC-failed)	0	0
Singletons	1730745	243407
Singletons(QC-failed)	0	0
% Singleton	0.9100	0.2100
Diff. Chroms	222181	163060
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	72237549	52001450
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	25055760	4546610
Paired Opt. Dupes	6264	7871
% Dupes/100	0.3469	0.0874

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	72229175	51125895
Distinct Read Pairs	47175632	46839993
One Read Pair	32629367	43009979
Two Read Pairs	8631032	3424215
NRF = Distinct/Total	0.6531	0.9162
PBC1 = OnePair/Distinct	0.6917	0.9182
PBC2 = OnePair/TwoPair	3.7805	12.5605

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	94363578	94909680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94363578	94909680
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	94363578	94909680
Paired(QC-failed)	0	0
Read1	47181789	47454840
Read1(QC-failed)	0	0
Read2	47181789	47454840
Read2(QC-failed)	0	0
Properly Paired	94363578	94909680
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	94363578	94909680
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	156683
Np	0
N optimal	156683
N conservative	156683
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.	200
Corr. Est. Fragment Len.	0.1713
Phantom Peak	50
Corr. Phantom Peak	0.2001
Argmin. Corr.	1500
Min. Corr.	0.1639
NSC	1.0449
RSC	0.2038

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	0.1312

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	0.2663
AUC	0.4958
CHANCE divergence	0.1265
Elbow Point	0.0000
JS Distance	0.5706
Synthetic AUC	0.5021
Synthetic Elbow Point	0.1420
Synthetic JS Distance	0.2947