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Report generated at 2022-01-06 08:06:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79195004	201652566
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78546733	198032065
Mapped(QC-failed)	0	0
% Mapped	99.1800	98.2000
Paired	79195004	201652566
Paired(QC-failed)	0	0
Read1	39597502	100826283
Read1(QC-failed)	0	0
Read2	39597502	100826283
Read2(QC-failed)	0	0
Properly Paired	77896509	194936556
Properly Paired(QC-failed)	0	0
% Properly Paired	98.3600	96.6700
With itself	78160288	196867125
With itself(QC-failed)	0	0
Singletons	386445	1164940
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.5800
Diff. Chroms	23800	328067
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	36393596	84633399
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2638071	1125235
Paired Opt. Dupes	1874	1306
% Dupes/100	0.0725	0.0133

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36385041	84626173
Distinct Read Pairs	33747523	83501515
One Read Pair	31735012	82459535
Two Read Pairs	1656442	999176
NRF = Distinct/Total	0.9275	0.9867
PBC1 = OnePair/Distinct	0.9404	0.9875
PBC2 = OnePair/TwoPair	19.1585	82.5275

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	67511050	167016328
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67511050	167016328
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67511050	167016328
Paired(QC-failed)	0	0
Read1	33755525	83508164
Read1(QC-failed)	0	0
Read2	33755525	83508164
Read2(QC-failed)	0	0
Properly Paired	67511050	167016328
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67511050	167016328
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	70119
Np	0
N optimal	70119
N conservative	70119
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.	155
Corr. Est. Fragment Len.	0.3274
Phantom Peak	55
Corr. Phantom Peak	0.2075
Argmin. Corr.	1500
Min. Corr.	0.1592
NSC	2.0563
RSC	3.4862

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	0.7257

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	0.0720
AUC	0.4950
CHANCE divergence	0.2477
Elbow Point	0.0000
JS Distance	0.9188
Synthetic AUC	0.5040
Synthetic Elbow Point	0.5905
Synthetic JS Distance	0.6711