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Report generated at 2019-10-13 04:35:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107237216	112182380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105498116	109790255
Mapped(QC-failed)	0	0
% Mapped	98.3800	97.8700
Paired	107237216	112182380
Paired(QC-failed)	0	0
Read1	53618608	56091190
Read1(QC-failed)	0	0
Read2	53618608	56091190
Read2(QC-failed)	0	0
Properly Paired	104532003	108525037
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4800	96.7400
With itself	104967449	109236441
With itself(QC-failed)	0	0
Singletons	530667	553814
Singletons(QC-failed)	0	0
% Singleton	0.4900	0.4900
Diff. Chroms	172512	375641
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	46773392	47985507
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4685770	3406633
Paired Opt. Dupes	7901	6387
% Dupes/100	0.1002	0.0710

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46771706	47950820
Distinct Read Pairs	42086117	44546891
One Read Pair	37861186	41387028
Two Read Pairs	3808603	2937039
NRF = Distinct/Total	0.8998	0.9290
PBC1 = OnePair/Distinct	0.8996	0.9291
PBC2 = OnePair/TwoPair	9.9410	14.0914

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	84175244	89157748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84175244	89157748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84175244	89157748
Paired(QC-failed)	0	0
Read1	42087622	44578874
Read1(QC-failed)	0	0
Read2	42087622	44578874
Read2(QC-failed)	0	0
Properly Paired	84175244	89157748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84175244	89157748
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	151952
Np	0
N optimal	151952
N conservative	151952
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.	0.1730
Phantom Peak	50
Corr. Phantom Peak	0.1812
Argmin. Corr.	1500
Min. Corr.	0.1693
NSC	1.0218
RSC	0.3103

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	0.2023

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	0.2665
AUC	0.4956
CHANCE divergence	0.1035
Elbow Point	0.0000
JS Distance	0.6466
Synthetic AUC	0.4970
Synthetic Elbow Point	0.1411
Synthetic JS Distance	0.3018