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Report generated at 2020-05-22 18:42:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96066248	101616908
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86507948	98299386
Mapped(QC-failed)	0	0
% Mapped	90.0500	96.7400
Paired	96066248	101616908
Paired(QC-failed)	0	0
Read1	48033124	50808454
Read1(QC-failed)	0	0
Read2	48033124	50808454
Read2(QC-failed)	0	0
Properly Paired	84931604	95630320
Properly Paired(QC-failed)	0	0
% Properly Paired	88.4100	94.1100
With itself	85793161	97482566
With itself(QC-failed)	0	0
Singletons	714787	816820
Singletons(QC-failed)	0	0
% Singleton	0.7400	0.8000
Diff. Chroms	370614	1199069
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	36240844	41555789
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	181652	219396
Paired Opt. Dupes	1431	598
% Dupes/100	0.0050	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36236899	41491091
Distinct Read Pairs	36055274	41273018
One Read Pair	35874817	41056255
Two Read Pairs	179325	215467
NRF = Distinct/Total	0.9950	0.9947
PBC1 = OnePair/Distinct	0.9950	0.9947
PBC2 = OnePair/TwoPair	200.0547	190.5454

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	72118384	82672786
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72118384	82672786
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72118384	82672786
Paired(QC-failed)	0	0
Read1	36059192	41336393
Read1(QC-failed)	0	0
Read2	36059192	41336393
Read2(QC-failed)	0	0
Properly Paired	72118384	82672786
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72118384	82672786
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	52907
Np	0
N optimal	52907
N conservative	52907
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.	105
Corr. Est. Fragment Len.	0.1858
Phantom Peak	50
Corr. Phantom Peak	0.2076
Argmin. Corr.	1500
Min. Corr.	0.1774
NSC	1.0476
RSC	0.2795

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	0.0376

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	0.2770
AUC	0.4952
CHANCE divergence	0.1038
Elbow Point	0.0000
JS Distance	0.5918
Synthetic AUC	0.4988
Synthetic Elbow Point	0.0445
Synthetic JS Distance	0.2822