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Report generated at 2020-05-20 13:08:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	73774622	202360194
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73472474	199280518
Mapped(QC-failed)	0	0
% Mapped	99.5900	98.4800
Paired	73774622	202360194
Paired(QC-failed)	0	0
Read1	36887311	101180097
Read1(QC-failed)	0	0
Read2	36887311	101180097
Read2(QC-failed)	0	0
Properly Paired	73300054	196010642
Properly Paired(QC-failed)	0	0
% Properly Paired	99.3600	96.8600
With itself	73354860	198492948
With itself(QC-failed)	0	0
Singletons	117614	787570
Singletons(QC-failed)	0	0
% Singleton	0.1600	0.3900
Diff. Chroms	11145	212946
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	34522955	87251527
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2804887	1128860
Paired Opt. Dupes	2554	5289
% Dupes/100	0.0812	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34510555	87198629
Distinct Read Pairs	31706391	86085041
One Read Pair	29816602	85022082
Two Read Pairs	1446313	1031715
NRF = Distinct/Total	0.9187	0.9872
PBC1 = OnePair/Distinct	0.9404	0.9877
PBC2 = OnePair/TwoPair	20.6156	82.4085

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	63436136	172245334
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63436136	172245334
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63436136	172245334
Paired(QC-failed)	0	0
Read1	31718068	86122667
Read1(QC-failed)	0	0
Read2	31718068	86122667
Read2(QC-failed)	0	0
Properly Paired	63436136	172245334
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63436136	172245334
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	87826
Np	0
N optimal	87826
N conservative	87826
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.	170
Corr. Est. Fragment Len.	0.3366
Phantom Peak	40
Corr. Phantom Peak	0.2078
Argmin. Corr.	1500
Min. Corr.	0.1393
NSC	2.4174
RSC	2.8786

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	0.7169

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	0.0652
AUC	0.4949
CHANCE divergence	0.3028
Elbow Point	0.0000
JS Distance	0.9053
Synthetic AUC	0.5068
Synthetic Elbow Point	0.5857
Synthetic JS Distance	0.6722