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Report generated at 2022-01-06 09:30:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	141932718	96892848
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139275480	95177952
Mapped(QC-failed)	0	0
% Mapped	98.1300	98.2300
Paired	141932718	96892848
Paired(QC-failed)	0	0
Read1	70966359	48446424
Read1(QC-failed)	0	0
Read2	70966359	48446424
Read2(QC-failed)	0	0
Properly Paired	137451610	93194189
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8400	96.1800
With itself	138040405	94492207
With itself(QC-failed)	0	0
Singletons	1235075	685745
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.7100
Diff. Chroms	95735	167050
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	58167870	40925417
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1172237	246447
Paired Opt. Dupes	3547	1202
% Dupes/100	0.0202	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58150568	40843756
Distinct Read Pairs	56979553	40626572
One Read Pair	55833925	40418029
Two Read Pairs	1123631	204865
NRF = Distinct/Total	0.9799	0.9947
PBC1 = OnePair/Distinct	0.9799	0.9949
PBC2 = OnePair/TwoPair	49.6906	197.2910

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	113991266	81357940
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113991266	81357940
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	113991266	81357940
Paired(QC-failed)	0	0
Read1	56995633	40678970
Read1(QC-failed)	0	0
Read2	56995633	40678970
Read2(QC-failed)	0	0
Properly Paired	113991266	81357940
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	113991266	81357940
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	90493
Np	0
N optimal	90493
N conservative	90493
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.	-10
Corr. Est. Fragment Len.	0.1830
Phantom Peak	50
Corr. Phantom Peak	0.1934
Argmin. Corr.	1500
Min. Corr.	0.1773
NSC	1.0320
RSC	0.3514

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	0.0776

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	0.2884
AUC	0.4962
CHANCE divergence	0.0946
Elbow Point	0.0000
JS Distance	0.5683
Synthetic AUC	0.5040
Synthetic Elbow Point	0.0850
Synthetic JS Distance	0.2721