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Report generated at 2020-11-21 00:07:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88891278	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87541191	187969057
Mapped(QC-failed)	0	0
% Mapped	98.4800	97.0900
Paired	88891278	193594802
Paired(QC-failed)	0	0
Read1	44445639	96797401
Read1(QC-failed)	0	0
Read2	44445639	96797401
Read2(QC-failed)	0	0
Properly Paired	86760437	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6000	95.1900
With itself	87076620	185784698
With itself(QC-failed)	0	0
Singletons	464571	2184359
Singletons(QC-failed)	0	0
% Singleton	0.5200	1.1300
Diff. Chroms	165396	610670
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	38544408	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15428721	539110
Paired Opt. Dupes	7682	19807
% Dupes/100	0.4003	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38415361	77646644
Distinct Read Pairs	23041480	77172156
One Read Pair	13617904	76701136
Two Read Pairs	5513665	467668
NRF = Distinct/Total	0.5998	0.9939
PBC1 = OnePair/Distinct	0.5910	0.9939
PBC2 = OnePair/TwoPair	2.4698	164.0077

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	46231374	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46231374	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46231374	155345422
Paired(QC-failed)	0	0
Read1	23115687	77672711
Read1(QC-failed)	0	0
Read2	23115687	77672711
Read2(QC-failed)	0	0
Properly Paired	46231374	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46231374	155345422
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	110781
Np	0
N optimal	110781
N conservative	110781
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.	265
Corr. Est. Fragment Len.	0.1615
Phantom Peak	50
Corr. Phantom Peak	0.1516
Argmin. Corr.	1500
Min. Corr.	0.1409
NSC	1.1458
RSC	1.9267

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	0.3651

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	0.1774
AUC	0.4940
CHANCE divergence	0.1923
Elbow Point	0.0000
JS Distance	0.7201
Synthetic AUC	0.4965
Synthetic Elbow Point	0.3197
Synthetic JS Distance	0.4255