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Report generated at 2019-10-25 17:45:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	135982452	108051026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	130436782	106769052
Mapped(QC-failed)	0	0
% Mapped	95.9200	98.8100
Paired	135982452	108051026
Paired(QC-failed)	0	0
Read1	67991226	54025513
Read1(QC-failed)	0	0
Read2	67991226	54025513
Read2(QC-failed)	0	0
Properly Paired	126695700	102974844
Properly Paired(QC-failed)	0	0
% Properly Paired	93.1700	95.3000
With itself	128876056	106137917
With itself(QC-failed)	0	0
Singletons	1560726	631135
Singletons(QC-failed)	0	0
% Singleton	1.1500	0.5800
Diff. Chroms	1363657	2007136
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	52158269	42899753
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3448983	909722
Paired Opt. Dupes	12915	7276
% Dupes/100	0.0661	0.0212

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52151483	42859157
Distinct Read Pairs	48702946	41950736
One Read Pair	45443662	41057737
Two Read Pairs	3079151	878320
NRF = Distinct/Total	0.9339	0.9788
PBC1 = OnePair/Distinct	0.9331	0.9787
PBC2 = OnePair/TwoPair	14.7585	46.7458

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	97418572	83980062
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97418572	83980062
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97418572	83980062
Paired(QC-failed)	0	0
Read1	48709286	41990031
Read1(QC-failed)	0	0
Read2	48709286	41990031
Read2(QC-failed)	0	0
Properly Paired	97418572	83980062
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97418572	83980062
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	181242
Np	0
N optimal	181242
N conservative	181242
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.	115
Corr. Est. Fragment Len.	0.1838
Phantom Peak	50
Corr. Phantom Peak	0.1899
Argmin. Corr.	1500
Min. Corr.	0.1804
NSC	1.0187
RSC	0.3558

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	0.1894

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	0.2215
AUC	0.4950
CHANCE divergence	0.1204
Elbow Point	0.0000
JS Distance	0.6560
Synthetic AUC	0.5039
Synthetic Elbow Point	0.1817
Synthetic JS Distance	0.3696