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Report generated at 2020-06-05 17:56:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77938600	126037706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73700399	123979523
Mapped(QC-failed)	0	0
% Mapped	94.5600	98.3700
Paired	77938600	126037706
Paired(QC-failed)	0	0
Read1	38969300	63018853
Read1(QC-failed)	0	0
Read2	38969300	63018853
Read2(QC-failed)	0	0
Properly Paired	73288186	122677160
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0300	97.3300
With itself	73465836	123316204
With itself(QC-failed)	0	0
Singletons	234563	663319
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.5300
Diff. Chroms	59328	230443
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	33775303	53582779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7146412	584944
Paired Opt. Dupes	2466	12360
% Dupes/100	0.2116	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33774108	53540225
Distinct Read Pairs	26627925	52956309
One Read Pair	21010912	52397141
Two Read Pairs	4408881	546325
NRF = Distinct/Total	0.7884	0.9891
PBC1 = OnePair/Distinct	0.7891	0.9894
PBC2 = OnePair/TwoPair	4.7656	95.9084

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	53257782	105995670
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53257782	105995670
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53257782	105995670
Paired(QC-failed)	0	0
Read1	26628891	52997835
Read1(QC-failed)	0	0
Read2	26628891	52997835
Read2(QC-failed)	0	0
Properly Paired	53257782	105995670
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53257782	105995670
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	126254
Np	0
N optimal	126254
N conservative	126254
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.	0.2140
Phantom Peak	50
Corr. Phantom Peak	0.2082
Argmin. Corr.	1500
Min. Corr.	0.1763
NSC	1.2140
RSC	1.1809

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	0.3503

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	0.1800
AUC	0.4944
CHANCE divergence	0.1660
Elbow Point	0.0000
JS Distance	0.7496
Synthetic AUC	0.4976
Synthetic Elbow Point	0.3309
Synthetic JS Distance	0.4405