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Report generated at 2020-05-22 16:18:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	44101066	145469574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42640464	141586568
Mapped(QC-failed)	0	0
% Mapped	96.6900	97.3300
Paired	44101066	145469574
Paired(QC-failed)	0	0
Read1	22050533	72734787
Read1(QC-failed)	0	0
Read2	22050533	72734787
Read2(QC-failed)	0	0
Properly Paired	42047825	139229482
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3400	95.7100
With itself	42467760	140814697
With itself(QC-failed)	0	0
Singletons	172704	771871
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.5300
Diff. Chroms	262821	836459
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	19044386	60565195
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	59102	282279
Paired Opt. Dupes	735	2180
% Dupes/100	0.0031	0.0047

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19043644	60530190
Distinct Read Pairs	18984547	60248362
One Read Pair	18925560	59967875
Two Read Pairs	58878	279160
NRF = Distinct/Total	0.9969	0.9953
PBC1 = OnePair/Distinct	0.9969	0.9953
PBC2 = OnePair/TwoPair	321.4369	214.8154

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	37970568	120565832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37970568	120565832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	37970568	120565832
Paired(QC-failed)	0	0
Read1	18985284	60282916
Read1(QC-failed)	0	0
Read2	18985284	60282916
Read2(QC-failed)	0	0
Properly Paired	37970568	120565832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	37970568	120565832
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	98675
Np	0
N optimal	98675
N conservative	98675
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.	135
Corr. Est. Fragment Len.	0.1846
Phantom Peak	50
Corr. Phantom Peak	0.1918
Argmin. Corr.	1500
Min. Corr.	0.1764
NSC	1.0467
RSC	0.5333

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	0.1621

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	0.2218
AUC	0.4934
CHANCE divergence	0.1649
Elbow Point	0.0000
JS Distance	0.6537
Synthetic AUC	0.5093
Synthetic Elbow Point	0.1617
Synthetic JS Distance	0.3458