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Report generated at 2019-10-12 19:20:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	84001186	88401972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81559398	86180692
Mapped(QC-failed)	0	0
% Mapped	97.0900	97.4900
Paired	84001186	88401972
Paired(QC-failed)	0	0
Read1	42000593	44200986
Read1(QC-failed)	0	0
Read2	42000593	44200986
Read2(QC-failed)	0	0
Properly Paired	80994942	85396352
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4200	96.6000
With itself	81211379	85734619
With itself(QC-failed)	0	0
Singletons	348019	446073
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.5000
Diff. Chroms	71991	70823
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	36934314	37252914
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9489480	7976046
Paired Opt. Dupes	20291	21511
% Dupes/100	0.2569	0.2141

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36932470	37214341
Distinct Read Pairs	27443418	29246499
One Read Pair	19005005	21451797
Two Read Pairs	7588502	7649880
NRF = Distinct/Total	0.7431	0.7859
PBC1 = OnePair/Distinct	0.6925	0.7335
PBC2 = OnePair/TwoPair	2.5044	2.8042

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	54889668	58553736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54889668	58553736
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54889668	58553736
Paired(QC-failed)	0	0
Read1	27444834	29276868
Read1(QC-failed)	0	0
Read2	27444834	29276868
Read2(QC-failed)	0	0
Properly Paired	54889668	58553736
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54889668	58553736
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	89318
Np	0
N optimal	89318
N conservative	89318
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.	185
Corr. Est. Fragment Len.	0.1616
Phantom Peak	50
Corr. Phantom Peak	0.1637
Argmin. Corr.	1500
Min. Corr.	0.1541
NSC	1.0483
RSC	0.7741

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	0.1728

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	0.2300
AUC	0.4945
CHANCE divergence	0.1422
Elbow Point	0.0000
JS Distance	0.6502
Synthetic AUC	0.5038
Synthetic Elbow Point	0.1488
Synthetic JS Distance	0.3462