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Report generated at 2022-09-02 12:06:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129002000	65769896
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84412965	64886900
Mapped(QC-failed)	0	0
% Mapped	65.4400	98.6600
Paired	129002000	65769896
Paired(QC-failed)	0	0
Read1	64501000	32884948
Read1(QC-failed)	0	0
Read2	64501000	32884948
Read2(QC-failed)	0	0
Properly Paired	83587646	64470476
Properly Paired(QC-failed)	0	0
% Properly Paired	64.8000	98.0200
With itself	84053607	64685111
With itself(QC-failed)	0	0
Singletons	359358	201789
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.3100
Diff. Chroms	53755	65977
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	37620380	28526999
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6083377	113439
Paired Opt. Dupes	5669	1566
% Dupes/100	0.1617	0.0040

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37619212	28513550
Distinct Read Pairs	31536017	28400237
One Read Pair	26346275	28288484
Two Read Pairs	4414967	110529
NRF = Distinct/Total	0.8383	0.9960
PBC1 = OnePair/Distinct	0.8354	0.9961
PBC2 = OnePair/TwoPair	5.9675	255.9372

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	63074006	56827120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63074006	56827120
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63074006	56827120
Paired(QC-failed)	0	0
Read1	31537003	28413560
Read1(QC-failed)	0	0
Read2	31537003	28413560
Read2(QC-failed)	0	0
Properly Paired	63074006	56827120
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63074006	56827120
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	143312
Np	0
N optimal	143312
N conservative	143312
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.	175
Corr. Est. Fragment Len.	0.1985
Phantom Peak	50
Corr. Phantom Peak	0.1967
Argmin. Corr.	1500
Min. Corr.	0.1797
NSC	1.1046
RSC	1.1086

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	0.3758

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	0.1703
AUC	0.4949
CHANCE divergence	0.1804
Elbow Point	0.0000
JS Distance	0.7283
Synthetic AUC	0.5008
Synthetic Elbow Point	0.3016
Synthetic JS Distance	0.4464