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Report generated at 2020-06-05 15:49:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	73238886	78469500
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71951486	76523645
Mapped(QC-failed)	0	0
% Mapped	98.2400	97.5200
Paired	73238886	78469500
Paired(QC-failed)	0	0
Read1	36619443	39234750
Read1(QC-failed)	0	0
Read2	36619443	39234750
Read2(QC-failed)	0	0
Properly Paired	71389363	74787695
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4700	95.3100
With itself	71650864	75995226
With itself(QC-failed)	0	0
Singletons	300622	528419
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.6700
Diff. Chroms	70976	142328
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	31865056	32771047
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6200132	449973
Paired Opt. Dupes	13029	9923
% Dupes/100	0.1946	0.0137

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31864661	32746475
Distinct Read Pairs	25664604	32297098
One Read Pair	20783646	31857228
Two Read Pairs	3854555	432385
NRF = Distinct/Total	0.8054	0.9863
PBC1 = OnePair/Distinct	0.8098	0.9864
PBC2 = OnePair/TwoPair	5.3920	73.6779

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	51329848	64642148
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51329848	64642148
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51329848	64642148
Paired(QC-failed)	0	0
Read1	25664924	32321074
Read1(QC-failed)	0	0
Read2	25664924	32321074
Read2(QC-failed)	0	0
Properly Paired	51329848	64642148
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51329848	64642148
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	143345
Np	0
N optimal	143345
N conservative	143345
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.	120
Corr. Est. Fragment Len.	0.1588
Phantom Peak	50
Corr. Phantom Peak	0.1601
Argmin. Corr.	1500
Min. Corr.	0.1542
NSC	1.0298
RSC	0.7703

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	0.0994

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	0.2385
AUC	0.4943
CHANCE divergence	0.1840
Elbow Point	0.0000
JS Distance	0.5954
Synthetic AUC	0.5011
Synthetic Elbow Point	0.1284
Synthetic JS Distance	0.3071