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Report generated at 2020-05-18 15:46:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	58720036	197624996
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56188303	192713678
Mapped(QC-failed)	0	0
% Mapped	95.6900	97.5100
Paired	58720036	197624996
Paired(QC-failed)	0	0
Read1	29360018	98812498
Read1(QC-failed)	0	0
Read2	29360018	98812498
Read2(QC-failed)	0	0
Properly Paired	55637199	189183779
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7500	95.7300
With itself	55998196	191730743
With itself(QC-failed)	0	0
Singletons	190107	982935
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.5000
Diff. Chroms	236896	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	25812122	82282989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	110482	411217
Paired Opt. Dupes	950	3070
% Dupes/100	0.0043	0.0050

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25811333	82255330
Distinct Read Pairs	25700856	81844454
One Read Pair	25590769	81439605
Two Read Pairs	109697	399981
NRF = Distinct/Total	0.9957	0.9950
PBC1 = OnePair/Distinct	0.9957	0.9951
PBC2 = OnePair/TwoPair	233.2860	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	51403280	163743544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51403280	163743544
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51403280	163743544
Paired(QC-failed)	0	0
Read1	25701640	81871772
Read1(QC-failed)	0	0
Read2	25701640	81871772
Read2(QC-failed)	0	0
Properly Paired	51403280	163743544
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51403280	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	132068
Np	0
N optimal	132068
N conservative	132068
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.	170
Corr. Est. Fragment Len.	0.2285
Phantom Peak	50
Corr. Phantom Peak	0.2245
Argmin. Corr.	1500
Min. Corr.	0.1968
NSC	1.1608
RSC	1.1436

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	0.4782

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	0.1301
AUC	0.4943
CHANCE divergence	0.2598
Elbow Point	0.0000
JS Distance	0.7734
Synthetic AUC	0.5034
Synthetic Elbow Point	0.3755
Synthetic JS Distance	0.4979