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Report generated at 2020-05-20 17:46:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	169239016	100538574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	168084408	98863286
Mapped(QC-failed)	0	0
% Mapped	99.3200	98.3300
Paired	169239016	100538574
Paired(QC-failed)	0	0
Read1	84619508	50269287
Read1(QC-failed)	0	0
Read2	84619508	50269287
Read2(QC-failed)	0	0
Properly Paired	167290084	94514238
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8500	94.0100
With itself	167413452	98221443
With itself(QC-failed)	0	0
Singletons	670956	641843
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.6400
Diff. Chroms	36803	127393
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	78197761	42061680
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2163078	280885
Paired Opt. Dupes	2793	1456
% Dupes/100	0.0277	0.0067

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	78195665	42052025
Distinct Read Pairs	76032649	41772167
One Read Pair	73965240	41504154
Two Read Pairs	1981184	263367
NRF = Distinct/Total	0.9723	0.9933
PBC1 = OnePair/Distinct	0.9728	0.9936
PBC2 = OnePair/TwoPair	37.3339	157.5906

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	152069366	83561590
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	152069366	83561590
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	152069366	83561590
Paired(QC-failed)	0	0
Read1	76034683	41780795
Read1(QC-failed)	0	0
Read2	76034683	41780795
Read2(QC-failed)	0	0
Properly Paired	152069366	83561590
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	152069366	83561590
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	246431
Np	0
N optimal	246431
N conservative	246431
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.	160
Corr. Est. Fragment Len.	0.1984
Phantom Peak	55
Corr. Phantom Peak	0.1863
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.1579
RSC	1.8073

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	0.5807

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	0.1453
AUC	0.4967
CHANCE divergence	0.1187
Elbow Point	0.0000
JS Distance	0.7929
Synthetic AUC	0.5019
Synthetic Elbow Point	0.3763
Synthetic JS Distance	0.5187