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Report generated at 2019-10-13 12:40:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	130336670	84831728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120292187	78378634
Mapped(QC-failed)	0	0
% Mapped	92.2900	92.3900
Paired	130336670	84831728
Paired(QC-failed)	0	0
Read1	65168335	42415864
Read1(QC-failed)	0	0
Read2	65168335	42415864
Read2(QC-failed)	0	0
Properly Paired	118822955	77370313
Properly Paired(QC-failed)	0	0
% Properly Paired	91.1700	91.2000
With itself	119880750	78051674
With itself(QC-failed)	0	0
Singletons	411437	326960
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.3900
Diff. Chroms	98341	132697
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	54990505	34106970
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6080591	361659
Paired Opt. Dupes	3264	2500
% Dupes/100	0.1106	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54988354	33930415
Distinct Read Pairs	48908016	33579942
One Read Pair	43398490	33235626
Two Read Pairs	4986832	339365
NRF = Distinct/Total	0.8894	0.9897
PBC1 = OnePair/Distinct	0.8873	0.9897
PBC2 = OnePair/TwoPair	8.7026	97.9347

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	97819828	67490622
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97819828	67490622
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97819828	67490622
Paired(QC-failed)	0	0
Read1	48909914	33745311
Read1(QC-failed)	0	0
Read2	48909914	33745311
Read2(QC-failed)	0	0
Properly Paired	97819828	67490622
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97819828	67490622
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	255534
Np	0
N optimal	255534
N conservative	255534
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.	125
Corr. Est. Fragment Len.	0.1786
Phantom Peak	50
Corr. Phantom Peak	0.1779
Argmin. Corr.	1500
Min. Corr.	0.1753
NSC	1.0191
RSC	1.2529

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	0.2874

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	0.1985
AUC	0.4959
CHANCE divergence	0.1502
Elbow Point	0.0000
JS Distance	0.6710
Synthetic AUC	0.5030
Synthetic Elbow Point	0.2407
Synthetic JS Distance	0.4012