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Report generated at 2020-05-13 08:23:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	55186482	57562006
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50844650	55523694
Mapped(QC-failed)	0	0
% Mapped	92.1300	96.4600
Paired	55186482	57562006
Paired(QC-failed)	0	0
Read1	27593241	28781003
Read1(QC-failed)	0	0
Read2	27593241	28781003
Read2(QC-failed)	0	0
Properly Paired	48089996	51717909
Properly Paired(QC-failed)	0	0
% Properly Paired	87.1400	89.8500
With itself	49754207	54506329
With itself(QC-failed)	0	0
Singletons	1090443	1017365
Singletons(QC-failed)	0	0
% Singleton	1.9800	1.7700
Diff. Chroms	579845	1879530
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	19173578	22692587
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	143853	223060
Paired Opt. Dupes	1960	2088
% Dupes/100	0.0075	0.0098

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19173225	22686649
Distinct Read Pairs	19029373	22463666
One Read Pair	18886517	22242527
Two Read Pairs	141871	219310
NRF = Distinct/Total	0.9925	0.9902
PBC1 = OnePair/Distinct	0.9925	0.9902
PBC2 = OnePair/TwoPair	133.1246	101.4205

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	38059450	44939054
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38059450	44939054
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38059450	44939054
Paired(QC-failed)	0	0
Read1	19029725	22469527
Read1(QC-failed)	0	0
Read2	19029725	22469527
Read2(QC-failed)	0	0
Properly Paired	38059450	44939054
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38059450	44939054
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	79948
Np	0
N optimal	79948
N conservative	79948
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.	250
Corr. Est. Fragment Len.	0.1907
Phantom Peak	50
Corr. Phantom Peak	0.2145
Argmin. Corr.	1500
Min. Corr.	0.1784
NSC	1.0688
RSC	0.3404

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	0.0869

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	0.2129
AUC	0.4934
CHANCE divergence	0.2549
Elbow Point	0.0000
JS Distance	0.6049
Synthetic AUC	0.4953
Synthetic Elbow Point	0.0542
Synthetic JS Distance	0.3165