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Report generated at 2019-11-03 19:08:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	150615902	158940554
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	145961188	157152767
Mapped(QC-failed)	0	0
% Mapped	96.9100	98.8800
Paired	150615902	158940554
Paired(QC-failed)	0	0
Read1	75307951	79470277
Read1(QC-failed)	0	0
Read2	75307951	79470277
Read2(QC-failed)	0	0
Properly Paired	142290229	154442853
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4700	97.1700
With itself	144507552	156399332
With itself(QC-failed)	0	0
Singletons	1453636	753435
Singletons(QC-failed)	0	0
% Singleton	0.9700	0.4700
Diff. Chroms	673616	1218211
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	50267248	68222921
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4008782	2746068
Paired Opt. Dupes	23029	28097
% Dupes/100	0.0797	0.0403

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50266400	68139154
Distinct Read Pairs	46257687	65397649
One Read Pair	42531995	62741963
Two Read Pairs	3468629	2573454
NRF = Distinct/Total	0.9203	0.9598
PBC1 = OnePair/Distinct	0.9195	0.9594
PBC2 = OnePair/TwoPair	12.2619	24.3804

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	92516932	130953706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92516932	130953706
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92516932	130953706
Paired(QC-failed)	0	0
Read1	46258466	65476853
Read1(QC-failed)	0	0
Read2	46258466	65476853
Read2(QC-failed)	0	0
Properly Paired	92516932	130953706
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92516932	130953706
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	243482
Np	0
N optimal	243482
N conservative	243482
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.	110
Corr. Est. Fragment Len.	0.2190
Phantom Peak	50
Corr. Phantom Peak	0.2611
Argmin. Corr.	1500
Min. Corr.	0.2081
NSC	1.0527
RSC	0.2067

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	0.6429

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	0.1166
AUC	0.4958
CHANCE divergence	0.2980
Elbow Point	0.0000
JS Distance	0.7554
Synthetic AUC	0.5036
Synthetic Elbow Point	0.4274
Synthetic JS Distance	0.5231