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Report generated at 2021-03-18 18:33:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	39971860	130013102
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33619435	126232097
Mapped(QC-failed)	0	0
% Mapped	84.1100	97.0900
Paired	39971860	130013102
Paired(QC-failed)	0	0
Read1	19985930	65006551
Read1(QC-failed)	0	0
Read2	19985930	65006551
Read2(QC-failed)	0	0
Properly Paired	32636793	109107434
Properly Paired(QC-failed)	0	0
% Properly Paired	81.6500	83.9200
With itself	33401540	124767100
With itself(QC-failed)	0	0
Singletons	217895	1464997
Singletons(QC-failed)	0	0
% Singleton	0.5500	1.1300
Diff. Chroms	160449	11420887
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	14718295	48591962
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1502525	535380
Paired Opt. Dupes	1385	1721
% Dupes/100	0.1021	0.0110

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	14715561	48585687
Distinct Read Pairs	13213308	48050759
One Read Pair	11861355	47543477
Two Read Pairs	1233243	492610
NRF = Distinct/Total	0.8979	0.9890
PBC1 = OnePair/Distinct	0.8977	0.9894
PBC2 = OnePair/TwoPair	9.6180	96.5134

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	26431540	96113164
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	26431540	96113164
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	26431540	96113164
Paired(QC-failed)	0	0
Read1	13215770	48056582
Read1(QC-failed)	0	0
Read2	13215770	48056582
Read2(QC-failed)	0	0
Properly Paired	26431540	96113164
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	26431540	96113164
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	58958
Np	0
N optimal	58958
N conservative	58958
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.	0.1933
Phantom Peak	50
Corr. Phantom Peak	0.1667
Argmin. Corr.	1500
Min. Corr.	0.1442
NSC	1.3407
RSC	2.1804

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	0.1604

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	0.2252
AUC	0.4921
CHANCE divergence	0.1966
Elbow Point	0.0000
JS Distance	0.6363
Synthetic AUC	0.5132
Synthetic Elbow Point	0.2138
Synthetic JS Distance	0.3367