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Report generated at 2020-05-18 10:48:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	43143000	168466658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42015238	164624745
Mapped(QC-failed)	0	0
% Mapped	97.3900	97.7200
Paired	43143000	168466658
Paired(QC-failed)	0	0
Read1	21571500	84233329
Read1(QC-failed)	0	0
Read2	21571500	84233329
Read2(QC-failed)	0	0
Properly Paired	41508186	162184918
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2100	96.2700
With itself	41858790	163825228
With itself(QC-failed)	0	0
Singletons	156448	799517
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.4700
Diff. Chroms	212617	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	18991240	70866978
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	60003	312582
Paired Opt. Dupes	492	1250
% Dupes/100	0.0032	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	18989653	70788047
Distinct Read Pairs	18929656	70477116
One Read Pair	18869768	70167781
Two Read Pairs	59779	307786
NRF = Distinct/Total	0.9968	0.9956
PBC1 = OnePair/Distinct	0.9968	0.9956
PBC2 = OnePair/TwoPair	315.6588	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	37862474	141108792
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37862474	141108792
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	37862474	141108792
Paired(QC-failed)	0	0
Read1	18931237	70554396
Read1(QC-failed)	0	0
Read2	18931237	70554396
Read2(QC-failed)	0	0
Properly Paired	37862474	141108792
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	37862474	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	100588
Np	0
N optimal	100588
N conservative	100588
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.	0.1862
Phantom Peak	50
Corr. Phantom Peak	0.1882
Argmin. Corr.	1500
Min. Corr.	0.1765
NSC	1.0552
RSC	0.8296

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	0.2128

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	0.2116
AUC	0.4934
CHANCE divergence	0.1729
Elbow Point	0.0000
JS Distance	0.6677
Synthetic AUC	0.4944
Synthetic Elbow Point	0.2193
Synthetic JS Distance	0.3627