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Report generated at 2021-10-21 14:25:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	117818720	271900510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115228435	268867859
Mapped(QC-failed)	0	0
% Mapped	97.8000	98.8800
Paired	117818720	271900510
Paired(QC-failed)	0	0
Read1	58909360	135950255
Read1(QC-failed)	0	0
Read2	58909360	135950255
Read2(QC-failed)	0	0
Properly Paired	112426929	243997757
Properly Paired(QC-failed)	0	0
% Properly Paired	95.4200	89.7400
With itself	113495271	266848954
With itself(QC-failed)	0	0
Singletons	1733164	2018905
Singletons(QC-failed)	0	0
% Singleton	1.4700	0.7400
Diff. Chroms	548111	17720672
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	48969327	102422784
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10195196	6269067
Paired Opt. Dupes	8240	15041
% Dupes/100	0.2082	0.0612

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48964549	102104617
Distinct Read Pairs	38770311	95885343
One Read Pair	30492306	90031317
Two Read Pairs	6685612	5511626
NRF = Distinct/Total	0.7918	0.9391
PBC1 = OnePair/Distinct	0.7865	0.9389
PBC2 = OnePair/TwoPair	4.5609	16.3348

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	77548262	192307434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77548262	192307434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	77548262	192307434
Paired(QC-failed)	0	0
Read1	38774131	96153717
Read1(QC-failed)	0	0
Read2	38774131	96153717
Read2(QC-failed)	0	0
Properly Paired	77548262	192307434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	77548262	192307434
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	200385
Np	0
N optimal	200385
N conservative	200385
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.	170
Corr. Est. Fragment Len.	0.1816
Phantom Peak	50
Corr. Phantom Peak	0.1797
Argmin. Corr.	1500
Min. Corr.	0.1697
NSC	1.0706
RSC	1.1914

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	0.4357

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	0.1824
AUC	0.4943
CHANCE divergence	0.1413
Elbow Point	0.0000
JS Distance	0.7504
Synthetic AUC	0.5062
Synthetic Elbow Point	0.3446
Synthetic JS Distance	0.4322