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Report generated at 2020-05-03 19:18:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98161700	144095950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88009550	133456854
Mapped(QC-failed)	0	0
% Mapped	89.6600	92.6200
Paired	98161700	144095950
Paired(QC-failed)	0	0
Read1	49080850	72047975
Read1(QC-failed)	0	0
Read2	49080850	72047975
Read2(QC-failed)	0	0
Properly Paired	81727984	100085786
Properly Paired(QC-failed)	0	0
% Properly Paired	83.2600	69.4600
With itself	85544510	127614780
With itself(QC-failed)	0	0
Singletons	2465040	5842074
Singletons(QC-failed)	0	0
% Singleton	2.5100	4.0500
Diff. Chroms	1945796	21841128
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	29504705	33283608
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	248167	401960
Paired Opt. Dupes	700	902
% Dupes/100	0.0084	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29472769	33264694
Distinct Read Pairs	29225045	32863263
One Read Pair	28982233	32466574
Two Read Pairs	238598	392011
NRF = Distinct/Total	0.9916	0.9879
PBC1 = OnePair/Distinct	0.9917	0.9879
PBC2 = OnePair/TwoPair	121.4689	82.8206

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	58513076	65763296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58513076	65763296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58513076	65763296
Paired(QC-failed)	0	0
Read1	29256538	32881648
Read1(QC-failed)	0	0
Read2	29256538	32881648
Read2(QC-failed)	0	0
Properly Paired	58513076	65763296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58513076	65763296
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	103518
Np	0
N optimal	103518
N conservative	103518
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.	130
Corr. Est. Fragment Len.	0.2108
Phantom Peak	50
Corr. Phantom Peak	0.2534
Argmin. Corr.	1500
Min. Corr.	0.1933
NSC	1.0906
RSC	0.2912

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	0.1262

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	0.2127
AUC	0.4947
CHANCE divergence	0.1985
Elbow Point	0.0000
JS Distance	0.6188
Synthetic AUC	0.5006
Synthetic Elbow Point	0.1301
Synthetic JS Distance	0.3553