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Report generated at 2020-12-04 04:59:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	180029910	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	177012470	187969057
Mapped(QC-failed)	0	0
% Mapped	98.3200	97.0900
Paired	180029910	193594802
Paired(QC-failed)	0	0
Read1	90014955	96797401
Read1(QC-failed)	0	0
Read2	90014955	96797401
Read2(QC-failed)	0	0
Properly Paired	174980540	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2000	95.1900
With itself	175802721	185784698
With itself(QC-failed)	0	0
Singletons	1209749	2184359
Singletons(QC-failed)	0	0
% Singleton	0.6700	1.1300
Diff. Chroms	429975	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	77296168	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1327856	539110
Paired Opt. Dupes	13082	19807
% Dupes/100	0.0172	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	77261995	77646644
Distinct Read Pairs	75934880	77172156
One Read Pair	74630121	76701136
Two Read Pairs	1282783	467668
NRF = Distinct/Total	0.9828	0.9939
PBC1 = OnePair/Distinct	0.9828	0.9939
PBC2 = OnePair/TwoPair	58.1783	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	151936624	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	151936624	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	151936624	155345422
Paired(QC-failed)	0	0
Read1	75968312	77672711
Read1(QC-failed)	0	0
Read2	75968312	77672711
Read2(QC-failed)	0	0
Properly Paired	151936624	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	151936624	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	175369
Np	0
N optimal	175369
N conservative	175369
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.	165
Corr. Est. Fragment Len.	0.2032
Phantom Peak	50
Corr. Phantom Peak	0.2035
Argmin. Corr.	1500
Min. Corr.	0.1835
NSC	1.1076
RSC	0.9871

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	0.3840

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	0.2110
AUC	0.4967
CHANCE divergence	0.1008
Elbow Point	0.0000
JS Distance	0.7379
Synthetic AUC	0.5032
Synthetic Elbow Point	0.3080
Synthetic JS Distance	0.4125