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Report generated at 2020-11-26 03:56:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	93731524	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92442375	187969057
Mapped(QC-failed)	0	0
% Mapped	98.6200	97.0900
Paired	93731524	193594802
Paired(QC-failed)	0	0
Read1	46865762	96797401
Read1(QC-failed)	0	0
Read2	46865762	96797401
Read2(QC-failed)	0	0
Properly Paired	91562432	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6900	95.1900
With itself	92079256	185784698
With itself(QC-failed)	0	0
Singletons	363119	2184359
Singletons(QC-failed)	0	0
% Singleton	0.3900	1.1300
Diff. Chroms	276110	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	41354178	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	836560	539110
Paired Opt. Dupes	5320	19807
% Dupes/100	0.0202	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41317856	77646644
Distinct Read Pairs	40482276	77172156
One Read Pair	39660556	76701136
Two Read Pairs	808070	467668
NRF = Distinct/Total	0.9798	0.9939
PBC1 = OnePair/Distinct	0.9797	0.9939
PBC2 = OnePair/TwoPair	49.0806	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	81035236	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81035236	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	81035236	155345422
Paired(QC-failed)	0	0
Read1	40517618	77672711
Read1(QC-failed)	0	0
Read2	40517618	77672711
Read2(QC-failed)	0	0
Properly Paired	81035236	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	81035236	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	144451
Np	0
N optimal	144451
N conservative	144451
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.	0.1988
Phantom Peak	50
Corr. Phantom Peak	0.1995
Argmin. Corr.	1500
Min. Corr.	0.1807
NSC	1.1000
RSC	0.9630

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	0.3179

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	0.2156
AUC	0.4955
CHANCE divergence	0.1181
Elbow Point	0.0000
JS Distance	0.7038
Synthetic AUC	0.4990
Synthetic Elbow Point	0.2862
Synthetic JS Distance	0.3927