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Report generated at 2020-05-18 20:10:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103278042	168466658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97949751	164624745
Mapped(QC-failed)	0	0
% Mapped	94.8400	97.7200
Paired	103278042	168466658
Paired(QC-failed)	0	0
Read1	51639021	84233329
Read1(QC-failed)	0	0
Read2	51639021	84233329
Read2(QC-failed)	0	0
Properly Paired	96360459	162184918
Properly Paired(QC-failed)	0	0
% Properly Paired	93.3000	96.2700
With itself	97292667	163825228
With itself(QC-failed)	0	0
Singletons	657084	799517
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.4700
Diff. Chroms	428296	775185
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	41561648	70866978
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	263990	312582
Paired Opt. Dupes	1719	1250
% Dupes/100	0.0064	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41556482	70788047
Distinct Read Pairs	41292537	70477116
One Read Pair	41030364	70167781
Two Read Pairs	260413	307786
NRF = Distinct/Total	0.9936	0.9956
PBC1 = OnePair/Distinct	0.9937	0.9956
PBC2 = OnePair/TwoPair	157.5588	227.9759

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	82595316	141108792
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82595316	141108792
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82595316	141108792
Paired(QC-failed)	0	0
Read1	41297658	70554396
Read1(QC-failed)	0	0
Read2	41297658	70554396
Read2(QC-failed)	0	0
Properly Paired	82595316	141108792
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82595316	141108792
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	122941
Np	0
N optimal	122941
N conservative	122941
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.	135
Corr. Est. Fragment Len.	0.1831
Phantom Peak	50
Corr. Phantom Peak	0.1996
Argmin. Corr.	1500
Min. Corr.	0.1752
NSC	1.0447
RSC	0.3208

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	0.1062

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	0.2644
AUC	0.4955
CHANCE divergence	0.1088
Elbow Point	0.0000
JS Distance	0.6050
Synthetic AUC	0.5033
Synthetic Elbow Point	0.1342
Synthetic JS Distance	0.3023