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Report generated at 2019-10-25 23:49:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171400538	175533488
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	168925935	173335768
Mapped(QC-failed)	0	0
% Mapped	98.5600	98.7500
Paired	171400538	175533488
Paired(QC-failed)	0	0
Read1	85700269	87766744
Read1(QC-failed)	0	0
Read2	85700269	87766744
Read2(QC-failed)	0	0
Properly Paired	164356109	163307962
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8900	93.0400
With itself	167882249	171954161
With itself(QC-failed)	0	0
Singletons	1043686	1381607
Singletons(QC-failed)	0	0
% Singleton	0.6100	0.7900
Diff. Chroms	2324594	6449643
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	67710447	68252842
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9041849	5232871
Paired Opt. Dupes	13173	11154
% Dupes/100	0.1335	0.0767

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	67710083	68242424
Distinct Read Pairs	58668287	63010354
One Read Pair	50646484	58070357
Two Read Pairs	7106516	4666317
NRF = Distinct/Total	0.8665	0.9233
PBC1 = OnePair/Distinct	0.8633	0.9216
PBC2 = OnePair/TwoPair	7.1268	12.4446

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	117337196	126039942
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117337196	126039942
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	117337196	126039942
Paired(QC-failed)	0	0
Read1	58668598	63019971
Read1(QC-failed)	0	0
Read2	58668598	63019971
Read2(QC-failed)	0	0
Properly Paired	117337196	126039942
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	117337196	126039942
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	157873
Np	0
N optimal	157873
N conservative	157873
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.	145
Corr. Est. Fragment Len.	0.1959
Phantom Peak	50
Corr. Phantom Peak	0.2028
Argmin. Corr.	1500
Min. Corr.	0.1885
NSC	1.0390
RSC	0.5151

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	0.2975

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	0.2119
AUC	0.4954
CHANCE divergence	0.1331
Elbow Point	0.0000
JS Distance	0.6645
Synthetic AUC	0.5043
Synthetic Elbow Point	0.2744
Synthetic JS Distance	0.3916