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Report generated at 2020-06-05 21:16:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	146483316	74925678
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139627142	73334040
Mapped(QC-failed)	0	0
% Mapped	95.3200	97.8800
Paired	146483316	74925678
Paired(QC-failed)	0	0
Read1	73241658	37462839
Read1(QC-failed)	0	0
Read2	73241658	37462839
Read2(QC-failed)	0	0
Properly Paired	137805916	72502624
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0800	96.7700
With itself	138492218	73039911
With itself(QC-failed)	0	0
Singletons	1134924	294129
Singletons(QC-failed)	0	0
% Singleton	0.7700	0.3900
Diff. Chroms	90265	216939
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	62068554	32127407
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8196818	360854
Paired Opt. Dupes	4301	4136
% Dupes/100	0.1321	0.0112

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62062463	31804933
Distinct Read Pairs	53866512	31477794
One Read Pair	46621001	31163507
Two Read Pairs	6393739	307462
NRF = Distinct/Total	0.8679	0.9897
PBC1 = OnePair/Distinct	0.8655	0.9900
PBC2 = OnePair/TwoPair	7.2917	101.3573

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	107743472	63533106
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107743472	63533106
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107743472	63533106
Paired(QC-failed)	0	0
Read1	53871736	31766553
Read1(QC-failed)	0	0
Read2	53871736	31766553
Read2(QC-failed)	0	0
Properly Paired	107743472	63533106
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107743472	63533106
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	199693
Np	0
N optimal	199693
N conservative	199693
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.	200
Corr. Est. Fragment Len.	0.1818
Phantom Peak	50
Corr. Phantom Peak	0.1870
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.0604
RSC	0.6652

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	0.3333

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	0.2245
AUC	0.4961
CHANCE divergence	0.1081
Elbow Point	0.0000
JS Distance	0.7245
Synthetic AUC	0.5039
Synthetic Elbow Point	0.2257
Synthetic JS Distance	0.3745