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Report generated at 2020-07-16 00:22:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	153873494	155229270
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	141306690	150942743
Mapped(QC-failed)	0	0
% Mapped	91.8300	97.2400
Paired	153873494	155229270
Paired(QC-failed)	0	0
Read1	76936747	77614635
Read1(QC-failed)	0	0
Read2	76936747	77614635
Read2(QC-failed)	0	0
Properly Paired	136924603	148607764
Properly Paired(QC-failed)	0	0
% Properly Paired	88.9900	95.7300
With itself	139073728	150154922
With itself(QC-failed)	0	0
Singletons	2232962	787821
Singletons(QC-failed)	0	0
% Singleton	1.4500	0.5100
Diff. Chroms	708376	787266
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	51296977	64735106
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	369427	274206
Paired Opt. Dupes	10596	1163
% Dupes/100	0.0072	0.0042

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51285368	64655208
Distinct Read Pairs	50916048	64382549
One Read Pair	50565274	64112121
Two Read Pairs	336733	268358
NRF = Distinct/Total	0.9928	0.9958
PBC1 = OnePair/Distinct	0.9931	0.9958
PBC2 = OnePair/TwoPair	150.1643	238.9052

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	101855100	128921800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101855100	128921800
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	101855100	128921800
Paired(QC-failed)	0	0
Read1	50927550	64460900
Read1(QC-failed)	0	0
Read2	50927550	64460900
Read2(QC-failed)	0	0
Properly Paired	101855100	128921800
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	101855100	128921800
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	175224
Np	0
N optimal	175224
N conservative	175224
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.	115
Corr. Est. Fragment Len.	0.1971
Phantom Peak	50
Corr. Phantom Peak	0.2458
Argmin. Corr.	1500
Min. Corr.	0.1843
NSC	1.0694
RSC	0.2079

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	0.1495

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	0.2729
AUC	0.4960
CHANCE divergence	0.1008
Elbow Point	0.0000
JS Distance	0.6075
Synthetic AUC	0.5023
Synthetic Elbow Point	0.1300
Synthetic JS Distance	0.2963