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Report generated at 2020-05-30 20:16:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	155942238	100267900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	154178268	98810235
Mapped(QC-failed)	0	0
% Mapped	98.8700	98.5500
Paired	155942238	100267900
Paired(QC-failed)	0	0
Read1	77971119	50133950
Read1(QC-failed)	0	0
Read2	77971119	50133950
Read2(QC-failed)	0	0
Properly Paired	134093771	95001401
Properly Paired(QC-failed)	0	0
% Properly Paired	85.9900	94.7500
With itself	153194926	98214055
With itself(QC-failed)	0	0
Singletons	983342	596180
Singletons(QC-failed)	0	0
% Singleton	0.6300	0.5900
Diff. Chroms	337711	104078
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	60288119	42286684
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2616580	312962
Paired Opt. Dupes	1398	1739
% Dupes/100	0.0434	0.0074

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60276091	42271898
Distinct Read Pairs	57660581	41960091
One Read Pair	55163451	41660400
Two Read Pairs	2391888	294709
NRF = Distinct/Total	0.9566	0.9926
PBC1 = OnePair/Distinct	0.9567	0.9929
PBC2 = OnePair/TwoPair	23.0627	141.3611

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	115343078	83947444
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115343078	83947444
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	115343078	83947444
Paired(QC-failed)	0	0
Read1	57671539	41973722
Read1(QC-failed)	0	0
Read2	57671539	41973722
Read2(QC-failed)	0	0
Properly Paired	115343078	83947444
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	115343078	83947444
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	216591
Np	0
N optimal	216591
N conservative	216591
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.	145
Corr. Est. Fragment Len.	0.1794
Phantom Peak	45
Corr. Phantom Peak	0.1775
Argmin. Corr.	1500
Min. Corr.	0.1724
NSC	1.0406
RSC	1.3737

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	0.1758

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	0.2357
AUC	0.4962
CHANCE divergence	0.1421
Elbow Point	0.0000
JS Distance	0.6018
Synthetic AUC	0.4978
Synthetic Elbow Point	0.1801
Synthetic JS Distance	0.3436