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Report generated at 2019-11-01 02:10:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71002236	317909612
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67142372	312072580
Mapped(QC-failed)	0	0
% Mapped	94.5600	98.1600
Paired	71002236	317909612
Paired(QC-failed)	0	0
Read1	35501118	158954806
Read1(QC-failed)	0	0
Read2	35501118	158954806
Read2(QC-failed)	0	0
Properly Paired	63588249	294728580
Properly Paired(QC-failed)	0	0
% Properly Paired	89.5600	92.7100
With itself	66594102	309884253
With itself(QC-failed)	0	0
Singletons	548270	2188327
Singletons(QC-failed)	0	0
% Singleton	0.7700	0.6900
Diff. Chroms	1700609	9012143
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	25792785	121497414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	19720590	13623598
Paired Opt. Dupes	8884	34172
% Dupes/100	0.7646	0.1121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25787234	121417759
Distinct Read Pairs	6070770	107806572
One Read Pair	1240308	95829671
Two Read Pairs	990863	10543184
NRF = Distinct/Total	0.2354	0.8879
PBC1 = OnePair/Distinct	0.2043	0.8889
PBC2 = OnePair/TwoPair	1.2517	9.0893

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	12144390	215747632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	12144390	215747632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	12144390	215747632
Paired(QC-failed)	0	0
Read1	6072195	107873816
Read1(QC-failed)	0	0
Read2	6072195	107873816
Read2(QC-failed)	0	0
Properly Paired	12144390	215747632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	12144390	215747632
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	61808
Np	0
N optimal	61808
N conservative	61808
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.	165
Corr. Est. Fragment Len.	0.1098
Phantom Peak	50
Corr. Phantom Peak	0.1072
Argmin. Corr.	1500
Min. Corr.	0.0721
NSC	1.5227
RSC	1.0735

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	0.3525

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	0.1170
AUC	0.4857
CHANCE divergence	0.4759
Elbow Point	0.0000
JS Distance	0.6697
Synthetic AUC	0.5260
Synthetic Elbow Point	0.3788
Synthetic JS Distance	0.4269