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Report generated at 2019-11-03 05:25:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	73793460	151544194
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72100656	148910512
Mapped(QC-failed)	0	0
% Mapped	97.7100	98.2600
Paired	73793460	151544194
Paired(QC-failed)	0	0
Read1	36896730	75772097
Read1(QC-failed)	0	0
Read2	36896730	75772097
Read2(QC-failed)	0	0
Properly Paired	71136015	146074541
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4000	96.3900
With itself	71752776	147974444
With itself(QC-failed)	0	0
Singletons	347880	936068
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.6200
Diff. Chroms	132686	884346
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	32690440	64801692
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4899902	1185579
Paired Opt. Dupes	6556	14661
% Dupes/100	0.1499	0.0183

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32684552	64733526
Distinct Read Pairs	27785553	63550092
One Read Pair	23505043	62385083
Two Read Pairs	3728379	1147263
NRF = Distinct/Total	0.8501	0.9817
PBC1 = OnePair/Distinct	0.8459	0.9817
PBC2 = OnePair/TwoPair	6.3044	54.3773

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	55581076	127232226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55581076	127232226
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55581076	127232226
Paired(QC-failed)	0	0
Read1	27790538	63616113
Read1(QC-failed)	0	0
Read2	27790538	63616113
Read2(QC-failed)	0	0
Properly Paired	55581076	127232226
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55581076	127232226
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	90836
Np	0
N optimal	90836
N conservative	90836
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.	0.1847
Phantom Peak	50
Corr. Phantom Peak	0.1837
Argmin. Corr.	1500
Min. Corr.	0.1637
NSC	1.1287
RSC	1.0496

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	0.3078

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	0.2152
AUC	0.4945
CHANCE divergence	0.1279
Elbow Point	0.0000
JS Distance	0.7152
Synthetic AUC	0.4979
Synthetic Elbow Point	0.2990
Synthetic JS Distance	0.3929