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Report generated at 2020-05-19 11:07:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	192711820	197624996
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	183540038	192713678
Mapped(QC-failed)	0	0
% Mapped	95.2400	97.5100
Paired	192711820	197624996
Paired(QC-failed)	0	0
Read1	96355910	98812498
Read1(QC-failed)	0	0
Read2	96355910	98812498
Read2(QC-failed)	0	0
Properly Paired	181547701	189183779
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2100	95.7300
With itself	182873534	191730743
With itself(QC-failed)	0	0
Singletons	666504	982935
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.5000
Diff. Chroms	850383	1513270
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	83913128	82282989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	724145	411217
Paired Opt. Dupes	3428	3070
% Dupes/100	0.0086	0.0050

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	83910162	82255330
Distinct Read Pairs	83186047	81844454
One Read Pair	82468052	81439605
Two Read Pairs	711926	399981
NRF = Distinct/Total	0.9914	0.9950
PBC1 = OnePair/Distinct	0.9914	0.9951
PBC2 = OnePair/TwoPair	115.8380	203.6087

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	166377966	163743544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	166377966	163743544
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	166377966	163743544
Paired(QC-failed)	0	0
Read1	83188983	81871772
Read1(QC-failed)	0	0
Read2	83188983	81871772
Read2(QC-failed)	0	0
Properly Paired	166377966	163743544
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	166377966	163743544
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	273308
Np	0
N optimal	273308
N conservative	273308
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.	140
Corr. Est. Fragment Len.	0.1955
Phantom Peak	50
Corr. Phantom Peak	0.1974
Argmin. Corr.	1500
Min. Corr.	0.1843
NSC	1.0610
RSC	0.8560

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	0.4994

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	0.1723
AUC	0.4968
CHANCE divergence	0.1184
Elbow Point	0.0000
JS Distance	0.7410
Synthetic AUC	0.4974
Synthetic Elbow Point	0.3220
Synthetic JS Distance	0.4651