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Report generated at 2021-02-05 14:23:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103699416	98018842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102844105	96270768
Mapped(QC-failed)	0	0
% Mapped	99.1800	98.2200
Paired	103699416	98018842
Paired(QC-failed)	0	0
Read1	51849708	49009421
Read1(QC-failed)	0	0
Read2	51849708	49009421
Read2(QC-failed)	0	0
Properly Paired	100253991	94403324
Properly Paired(QC-failed)	0	0
% Properly Paired	96.6800	96.3100
With itself	102288453	95481141
With itself(QC-failed)	0	0
Singletons	555652	789627
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.8100
Diff. Chroms	59301	119737
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	46705281	40573634
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	430218	190324
Paired Opt. Dupes	1027	892
% Dupes/100	0.0092	0.0047

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46697632	40559437
Distinct Read Pairs	46267645	40369743
One Read Pair	45845067	40192163
Two Read Pairs	415625	172878
NRF = Distinct/Total	0.9908	0.9953
PBC1 = OnePair/Distinct	0.9909	0.9956
PBC2 = OnePair/TwoPair	110.3039	232.4886

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	92550126	80766620
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92550126	80766620
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92550126	80766620
Paired(QC-failed)	0	0
Read1	46275063	40383310
Read1(QC-failed)	0	0
Read2	46275063	40383310
Read2(QC-failed)	0	0
Properly Paired	92550126	80766620
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92550126	80766620
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	238730
Np	0
N optimal	238730
N conservative	238730
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.	145
Corr. Est. Fragment Len.	0.1866
Phantom Peak	55
Corr. Phantom Peak	0.1804
Argmin. Corr.	1500
Min. Corr.	0.1707
NSC	1.0936
RSC	1.6414

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	0.3877

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	0.1974
AUC	0.4956
CHANCE divergence	0.1222
Elbow Point	0.0000
JS Distance	0.7460
Synthetic AUC	0.5061
Synthetic Elbow Point	0.2268
Synthetic JS Distance	0.4140