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Report generated at 2019-10-25 16:49:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79905464	164317158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73246548	162006082
Mapped(QC-failed)	0	0
% Mapped	91.6700	98.5900
Paired	79905464	164317158
Paired(QC-failed)	0	0
Read1	39952732	82158579
Read1(QC-failed)	0	0
Read2	39952732	82158579
Read2(QC-failed)	0	0
Properly Paired	71793015	158686405
Properly Paired(QC-failed)	0	0
% Properly Paired	89.8500	96.5700
With itself	72483415	161193128
With itself(QC-failed)	0	0
Singletons	763133	812954
Singletons(QC-failed)	0	0
% Singleton	0.9600	0.4900
Diff. Chroms	392452	1201289
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	31706259	66502967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2517142	1918147
Paired Opt. Dupes	9758	14289
% Dupes/100	0.0794	0.0288

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31704459	66493940
Distinct Read Pairs	29187461	64576078
One Read Pair	26833329	62704334
Two Read Pairs	2200418	1827454
NRF = Distinct/Total	0.9206	0.9712
PBC1 = OnePair/Distinct	0.9193	0.9710
PBC2 = OnePair/TwoPair	12.1947	34.3124

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	58378234	129169640
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58378234	129169640
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58378234	129169640
Paired(QC-failed)	0	0
Read1	29189117	64584820
Read1(QC-failed)	0	0
Read2	29189117	64584820
Read2(QC-failed)	0	0
Properly Paired	58378234	129169640
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58378234	129169640
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	60804
Np	0
N optimal	60804
N conservative	60804
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.	165
Corr. Est. Fragment Len.	0.2697
Phantom Peak	50
Corr. Phantom Peak	0.2608
Argmin. Corr.	1500
Min. Corr.	0.1927
NSC	1.3998
RSC	1.1312

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	0.4685

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	0.1558
AUC	0.4937
CHANCE divergence	0.1490
Elbow Point	0.0000
JS Distance	0.8343
Synthetic AUC	0.5104
Synthetic Elbow Point	0.4363
Synthetic JS Distance	0.5106