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Report generated at 2020-04-08 15:10:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104813642	52163906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100813382	51011228
Mapped(QC-failed)	0	0
% Mapped	96.1800	97.7900
Paired	104813642	52163906
Paired(QC-failed)	0	0
Read1	52406821	26081953
Read1(QC-failed)	0	0
Read2	52406821	26081953
Read2(QC-failed)	0	0
Properly Paired	99615700	50327448
Properly Paired(QC-failed)	0	0
% Properly Paired	95.0400	96.4800
With itself	100013074	50605280
With itself(QC-failed)	0	0
Singletons	800308	405948
Singletons(QC-failed)	0	0
% Singleton	0.7600	0.7800
Diff. Chroms	114875	116270
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	42627876	21583217
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4033210	577625
Paired Opt. Dupes	4481	1859
% Dupes/100	0.0946	0.0268

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42627074	21564764
Distinct Read Pairs	38593925	20987719
One Read Pair	34960443	20426444
Two Read Pairs	3274815	546386
NRF = Distinct/Total	0.9054	0.9732
PBC1 = OnePair/Distinct	0.9059	0.9733
PBC2 = OnePair/TwoPair	10.6755	37.3846

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	77189332	42011184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77189332	42011184
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	77189332	42011184
Paired(QC-failed)	0	0
Read1	38594666	21005592
Read1(QC-failed)	0	0
Read2	38594666	21005592
Read2(QC-failed)	0	0
Properly Paired	77189332	42011184
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	77189332	42011184
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	43423
Np	0
N optimal	43423
N conservative	43423
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.	185
Corr. Est. Fragment Len.	0.1700
Phantom Peak	50
Corr. Phantom Peak	0.1791
Argmin. Corr.	1500
Min. Corr.	0.1660
NSC	1.0240
RSC	0.3041

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	0.3033
AUC	0.4954
CHANCE divergence	0.1089
Elbow Point	0.0000
JS Distance	0.5443
Synthetic AUC	0.4957
Synthetic Elbow Point	0.0410
Synthetic JS Distance	0.2382