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Report generated at 2020-05-21 04:56:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	172113158	172040776
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135055684	166313177
Mapped(QC-failed)	0	0
% Mapped	78.4700	96.6700
Paired	172113158	172040776
Paired(QC-failed)	0	0
Read1	86056579	86020388
Read1(QC-failed)	0	0
Read2	86056579	86020388
Read2(QC-failed)	0	0
Properly Paired	133123969	164316966
Properly Paired(QC-failed)	0	0
% Properly Paired	77.3500	95.5100
With itself	133883362	165368990
With itself(QC-failed)	0	0
Singletons	1172322	944187
Singletons(QC-failed)	0	0
% Singleton	0.6800	0.5500
Diff. Chroms	311187	377471
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	58023874	70615481
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	604998	448995
Paired Opt. Dupes	1537	1973
% Dupes/100	0.0104	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58016628	70604488
Distinct Read Pairs	57411721	70155597
One Read Pair	56813981	69710274
Two Read Pairs	590714	441873
NRF = Distinct/Total	0.9896	0.9936
PBC1 = OnePair/Distinct	0.9896	0.9937
PBC2 = OnePair/TwoPair	96.1785	157.7609

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	114837752	140332972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114837752	140332972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	114837752	140332972
Paired(QC-failed)	0	0
Read1	57418876	70166486
Read1(QC-failed)	0	0
Read2	57418876	70166486
Read2(QC-failed)	0	0
Properly Paired	114837752	140332972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	114837752	140332972
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	216902
Np	0
N optimal	216902
N conservative	216902
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.	150
Corr. Est. Fragment Len.	0.1893
Phantom Peak	50
Corr. Phantom Peak	0.2115
Argmin. Corr.	1500
Min. Corr.	0.1781
NSC	1.0629
RSC	0.3351

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	0.2558

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	0.2362
AUC	0.4962
CHANCE divergence	0.1079
Elbow Point	0.0000
JS Distance	0.6519
Synthetic AUC	0.5039
Synthetic Elbow Point	0.1735
Synthetic JS Distance	0.3545