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Report generated at 2020-05-19 00:40:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123362796	137038710
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112094293	132965142
Mapped(QC-failed)	0	0
% Mapped	90.8700	97.0300
Paired	123362796	137038710
Paired(QC-failed)	0	0
Read1	61681398	68519355
Read1(QC-failed)	0	0
Read2	61681398	68519355
Read2(QC-failed)	0	0
Properly Paired	109069986	130403765
Properly Paired(QC-failed)	0	0
% Properly Paired	88.4100	95.1600
With itself	110519149	132147488
With itself(QC-failed)	0	0
Singletons	1575144	817654
Singletons(QC-failed)	0	0
% Singleton	1.2800	0.6000
Diff. Chroms	468301	1017994
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	41373250	56489373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	233588	246609
Paired Opt. Dupes	1447	1947
% Dupes/100	0.0056	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41367981	56440954
Distinct Read Pairs	41134430	56195118
One Read Pair	40904603	55950441
Two Read Pairs	226512	243541
NRF = Distinct/Total	0.9944	0.9956
PBC1 = OnePair/Distinct	0.9944	0.9956
PBC2 = OnePair/TwoPair	180.5847	229.7373

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	82279324	112485528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82279324	112485528
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82279324	112485528
Paired(QC-failed)	0	0
Read1	41139662	56242764
Read1(QC-failed)	0	0
Read2	41139662	56242764
Read2(QC-failed)	0	0
Properly Paired	82279324	112485528
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82279324	112485528
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	115281
Np	0
N optimal	115281
N conservative	115281
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.	0.1990
Phantom Peak	50
Corr. Phantom Peak	0.2428
Argmin. Corr.	1500
Min. Corr.	0.1875
NSC	1.0610
RSC	0.2068

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	0.0966

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	0.2836
AUC	0.4955
CHANCE divergence	0.0981
Elbow Point	0.0000
JS Distance	0.5921
Synthetic AUC	0.4967
Synthetic Elbow Point	0.0728
Synthetic JS Distance	0.2779