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Report generated at 2021-10-10 00:17:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	156011528	123193466
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129989307	118923949
Mapped(QC-failed)	0	0
% Mapped	83.3200	96.5300
Paired	156011528	123193466
Paired(QC-failed)	0	0
Read1	78005764	61596733
Read1(QC-failed)	0	0
Read2	78005764	61596733
Read2(QC-failed)	0	0
Properly Paired	128789644	116106964
Properly Paired(QC-failed)	0	0
% Properly Paired	82.5500	94.2500
With itself	129211832	118122229
With itself(QC-failed)	0	0
Singletons	777475	801720
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6500
Diff. Chroms	277515	1326630
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	58526298	48288802
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16387591	2118238
Paired Opt. Dupes	31237	32462
% Dupes/100	0.2800	0.0439

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58525630	48279257
Distinct Read Pairs	42138235	46161447
One Read Pair	29879917	44113515
Two Read Pairs	9091243	1980535
NRF = Distinct/Total	0.7200	0.9561
PBC1 = OnePair/Distinct	0.7091	0.9556
PBC2 = OnePair/TwoPair	3.2867	22.2735

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	84277414	92341128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84277414	92341128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84277414	92341128
Paired(QC-failed)	0	0
Read1	42138707	46170564
Read1(QC-failed)	0	0
Read2	42138707	46170564
Read2(QC-failed)	0	0
Properly Paired	84277414	92341128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84277414	92341128
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	44451
Np	0
N optimal	44451
N conservative	44451
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.	210
Corr. Est. Fragment Len.	0.4897
Phantom Peak	55
Corr. Phantom Peak	0.4392
Argmin. Corr.	1500
Min. Corr.	0.1937
NSC	2.5279
RSC	1.2057

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	0.7854

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	0.0501
AUC	0.4946
CHANCE divergence	0.2741
Elbow Point	0.0000
JS Distance	0.9481
Synthetic AUC	0.4972
Synthetic Elbow Point	0.6910
Synthetic JS Distance	0.7404