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Report generated at 2020-05-13 03:51:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	69251344	44822058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65682465	42270277
Mapped(QC-failed)	0	0
% Mapped	94.8500	94.3100
Paired	69251344	44822058
Paired(QC-failed)	0	0
Read1	34625672	22411029
Read1(QC-failed)	0	0
Read2	34625672	22411029
Read2(QC-failed)	0	0
Properly Paired	63025696	39106937
Properly Paired(QC-failed)	0	0
% Properly Paired	91.0100	87.2500
With itself	64763403	41498214
With itself(QC-failed)	0	0
Singletons	919062	772063
Singletons(QC-failed)	0	0
% Singleton	1.3300	1.7200
Diff. Chroms	1337787	1698756
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	28431119	17000414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	208949	184749
Paired Opt. Dupes	2745	1571
% Dupes/100	0.0073	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28430857	16997550
Distinct Read Pairs	28221909	16812850
One Read Pair	28014288	16629884
Two Read Pairs	206300	181248
NRF = Distinct/Total	0.9927	0.9891
PBC1 = OnePair/Distinct	0.9926	0.9891
PBC2 = OnePair/TwoPair	135.7939	91.7521

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	56444340	33631330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56444340	33631330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56444340	33631330
Paired(QC-failed)	0	0
Read1	28222170	16815665
Read1(QC-failed)	0	0
Read2	28222170	16815665
Read2(QC-failed)	0	0
Properly Paired	56444340	33631330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56444340	33631330
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	95520
Np	0
N optimal	95520
N conservative	95520
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.	270
Corr. Est. Fragment Len.	0.2017
Phantom Peak	50
Corr. Phantom Peak	0.1924
Argmin. Corr.	1500
Min. Corr.	0.1839
NSC	1.0969
RSC	2.0976

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	0.2011

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	0.1393
AUC	0.4945
CHANCE divergence	0.3993
Elbow Point	0.0000
JS Distance	0.6814
Synthetic AUC	0.5050
Synthetic Elbow Point	0.1201
Synthetic JS Distance	0.4063