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Report generated at 2019-10-13 00:40:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	66681824	125060354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65415735	115723438
Mapped(QC-failed)	0	0
% Mapped	98.1000	92.5300
Paired	66681824	125060354
Paired(QC-failed)	0	0
Read1	33340912	62530177
Read1(QC-failed)	0	0
Read2	33340912	62530177
Read2(QC-failed)	0	0
Properly Paired	64507382	106456049
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7400	85.1200
With itself	64873673	108232132
With itself(QC-failed)	0	0
Singletons	542062	7491306
Singletons(QC-failed)	0	0
% Singleton	0.8100	5.9900
Diff. Chroms	180305	1197727
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	27718603	42322290
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	545554	491333
Paired Opt. Dupes	2826	3358
% Dupes/100	0.0197	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27718066	42292215
Distinct Read Pairs	27172518	41801473
One Read Pair	26637021	41322617
Two Read Pairs	525715	470011
NRF = Distinct/Total	0.9803	0.9884
PBC1 = OnePair/Distinct	0.9803	0.9885
PBC2 = OnePair/TwoPair	50.6682	87.9184

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	54346098	83661914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54346098	83661914
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54346098	83661914
Paired(QC-failed)	0	0
Read1	27173049	41830957
Read1(QC-failed)	0	0
Read2	27173049	41830957
Read2(QC-failed)	0	0
Properly Paired	54346098	83661914
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54346098	83661914
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	123923
Np	0
N optimal	123923
N conservative	123923
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.	130
Corr. Est. Fragment Len.	0.1753
Phantom Peak	50
Corr. Phantom Peak	0.1851
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.0199
RSC	0.2586

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	0.1623

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	0.2608
AUC	0.4945
CHANCE divergence	0.1199
Elbow Point	0.0000
JS Distance	0.6282
Synthetic AUC	0.5004
Synthetic Elbow Point	0.1517
Synthetic JS Distance	0.3001