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Report generated at 2020-05-27 15:29:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	160831448	185333438
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80005196	179322251
Mapped(QC-failed)	0	0
% Mapped	49.7400	96.7600
Paired	160831448	185333438
Paired(QC-failed)	0	0
Read1	80415724	92666719
Read1(QC-failed)	0	0
Read2	80415724	92666719
Read2(QC-failed)	0	0
Properly Paired	77783374	177236646
Properly Paired(QC-failed)	0	0
% Properly Paired	48.3600	95.6300
With itself	78218114	178226497
With itself(QC-failed)	0	0
Singletons	1787082	1095754
Singletons(QC-failed)	0	0
% Singleton	1.1100	0.5900
Diff. Chroms	112479	321793
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	34180257	76478349
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	769281	700148
Paired Opt. Dupes	1531	1938
% Dupes/100	0.0225	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34176062	76473537
Distinct Read Pairs	33406891	75773440
One Read Pair	32655168	75080087
Two Read Pairs	734647	686711
NRF = Distinct/Total	0.9775	0.9908
PBC1 = OnePair/Distinct	0.9775	0.9909
PBC2 = OnePair/TwoPair	44.4501	109.3329

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	66821952	151556402
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66821952	151556402
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66821952	151556402
Paired(QC-failed)	0	0
Read1	33410976	75778201
Read1(QC-failed)	0	0
Read2	33410976	75778201
Read2(QC-failed)	0	0
Properly Paired	66821952	151556402
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66821952	151556402
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	59845
Np	0
N optimal	59845
N conservative	59845
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.	140
Corr. Est. Fragment Len.	0.1823
Phantom Peak	50
Corr. Phantom Peak	0.2300
Argmin. Corr.	1500
Min. Corr.	0.1636
NSC	1.1143
RSC	0.2816

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	0.1512

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	0.2389
AUC	0.4950
CHANCE divergence	0.1265
Elbow Point	0.0000
JS Distance	0.6314
Synthetic AUC	0.4958
Synthetic Elbow Point	0.1649
Synthetic JS Distance	0.3467