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Report generated at 2020-06-05 22:18:33

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	110160394	121920692
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105876530	119191863
Mapped(QC-failed)	0	0
% Mapped	96.1100	97.7600
Paired	110160394	121920692
Paired(QC-failed)	0	0
Read1	55080197	60960346
Read1(QC-failed)	0	0
Read2	55080197	60960346
Read2(QC-failed)	0	0
Properly Paired	104197422	117754194
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5900	96.5800
With itself	104776438	118308645
With itself(QC-failed)	0	0
Singletons	1100092	883218
Singletons(QC-failed)	0	0
% Singleton	1.0000	0.7200
Diff. Chroms	123695	122186
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	43561184	50862870
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17256070	879406
Paired Opt. Dupes	6270	8068
% Dupes/100	0.3961	0.0173

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43558925	50817650
Distinct Read Pairs	26303548	49939924
One Read Pair	16891103	49088463
Two Read Pairs	5438102	832695
NRF = Distinct/Total	0.6039	0.9827
PBC1 = OnePair/Distinct	0.6422	0.9829
PBC2 = OnePair/TwoPair	3.1061	58.9513

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	52610228	99966928
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52610228	99966928
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52610228	99966928
Paired(QC-failed)	0	0
Read1	26305114	49983464
Read1(QC-failed)	0	0
Read2	26305114	49983464
Read2(QC-failed)	0	0
Properly Paired	52610228	99966928
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52610228	99966928
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	88787
Np	0
N optimal	88787
N conservative	88787
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.	150
Corr. Est. Fragment Len.	0.1676
Phantom Peak	50
Corr. Phantom Peak	0.1862
Argmin. Corr.	1500
Min. Corr.	0.1534
NSC	1.0922
RSC	0.4311

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	0.1504

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	0.2388
AUC	0.4944
CHANCE divergence	0.1514
Elbow Point	0.0000
JS Distance	0.6188
Synthetic AUC	0.5094
Synthetic Elbow Point	0.1358
Synthetic JS Distance	0.3285