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Report generated at 2020-06-07 21:22:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	235229500	81954026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	223302833	79524453
Mapped(QC-failed)	0	0
% Mapped	94.9300	97.0400
Paired	235229500	81954026
Paired(QC-failed)	0	0
Read1	117614750	40977013
Read1(QC-failed)	0	0
Read2	117614750	40977013
Read2(QC-failed)	0	0
Properly Paired	221402975	77093809
Properly Paired(QC-failed)	0	0
% Properly Paired	94.1200	94.0700
With itself	222401766	79098582
With itself(QC-failed)	0	0
Singletons	901067	425871
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5200
Diff. Chroms	311980	1402675
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	98581518	34184322
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1419638	147586
Paired Opt. Dupes	9825	4439
% Dupes/100	0.0144	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	98579015	34160608
Distinct Read Pairs	97159416	34013271
One Read Pair	95762542	33871853
Two Read Pairs	1375540	138097
NRF = Distinct/Total	0.9856	0.9957
PBC1 = OnePair/Distinct	0.9856	0.9958
PBC2 = OnePair/TwoPair	69.6181	245.2758

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	194323760	68073472
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	194323760	68073472
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	194323760	68073472
Paired(QC-failed)	0	0
Read1	97161880	34036736
Read1(QC-failed)	0	0
Read2	97161880	34036736
Read2(QC-failed)	0	0
Properly Paired	194323760	68073472
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	194323760	68073472
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	120988
Np	0
N optimal	120988
N conservative	120988
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.	125
Corr. Est. Fragment Len.	0.1779
Phantom Peak	50
Corr. Phantom Peak	0.1875
Argmin. Corr.	1500
Min. Corr.	0.1727
NSC	1.0298
RSC	0.3473

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	0.1141

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	0.3189
AUC	0.4971
CHANCE divergence	0.0966
Elbow Point	0.0000
JS Distance	0.5847
Synthetic AUC	0.4977
Synthetic Elbow Point	0.0948
Synthetic JS Distance	0.2302