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Report generated at 2019-10-26 20:35:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120648984	300510464
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118937704	296808102
Mapped(QC-failed)	0	0
% Mapped	98.5800	98.7700
Paired	120648984	300510464
Paired(QC-failed)	0	0
Read1	60324492	150255232
Read1(QC-failed)	0	0
Read2	60324492	150255232
Read2(QC-failed)	0	0
Properly Paired	116708308	288771153
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7300	96.0900
With itself	118320912	295113278
With itself(QC-failed)	0	0
Singletons	616792	1694824
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.5600
Diff. Chroms	556048	3152209
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	49277898	118171618
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10791679	10537238
Paired Opt. Dupes	16322	30995
% Dupes/100	0.2190	0.0892

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49263686	118065463
Distinct Read Pairs	38474986	107541701
One Read Pair	29935393	97935810
Two Read Pairs	6724876	8765323
NRF = Distinct/Total	0.7810	0.9109
PBC1 = OnePair/Distinct	0.7780	0.9107
PBC2 = OnePair/TwoPair	4.4514	11.1731

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	76972438	215268760
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76972438	215268760
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76972438	215268760
Paired(QC-failed)	0	0
Read1	38486219	107634380
Read1(QC-failed)	0	0
Read2	38486219	107634380
Read2(QC-failed)	0	0
Properly Paired	76972438	215268760
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76972438	215268760
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	108646
Np	0
N optimal	108646
N conservative	108646
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.	200
Corr. Est. Fragment Len.	0.1660
Phantom Peak	50
Corr. Phantom Peak	0.1706
Argmin. Corr.	1500
Min. Corr.	0.1598
NSC	1.0388
RSC	0.5748

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	0.2372

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	0.2544
AUC	0.4943
CHANCE divergence	0.1160
Elbow Point	0.0000
JS Distance	0.6524
Synthetic AUC	0.4963
Synthetic Elbow Point	0.2244
Synthetic JS Distance	0.3197