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Report generated at 2020-12-04 01:16:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	161949614	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	157675568	143500908
Mapped(QC-failed)	0	0
% Mapped	97.3600	96.7800
Paired	161949614	148269018
Paired(QC-failed)	0	0
Read1	80974807	74134509
Read1(QC-failed)	0	0
Read2	80974807	74134509
Read2(QC-failed)	0	0
Properly Paired	155134937	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7900	94.5800
With itself	156601364	141622671
With itself(QC-failed)	0	0
Singletons	1074204	1878237
Singletons(QC-failed)	0	0
% Singleton	0.6600	1.2700
Diff. Chroms	756134	652729
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	68265160	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	274200	523701
Paired Opt. Dupes	10832	14446
% Dupes/100	0.0040	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68225384	57674075
Distinct Read Pairs	67951569	57472830
One Read Pair	67679241	57272993
Two Read Pairs	270916	198503
NRF = Distinct/Total	0.9960	0.9965
PBC1 = OnePair/Distinct	0.9960	0.9965
PBC2 = OnePair/TwoPair	249.8163	288.5246

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	135981920	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135981920	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	135981920	117133936
Paired(QC-failed)	0	0
Read1	67990960	58566968
Read1(QC-failed)	0	0
Read2	67990960	58566968
Read2(QC-failed)	0	0
Properly Paired	135981920	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	135981920	117133936
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	78439
Np	0
N optimal	78439
N conservative	78439
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.	140
Corr. Est. Fragment Len.	0.1880
Phantom Peak	50
Corr. Phantom Peak	0.2043
Argmin. Corr.	1500
Min. Corr.	0.1781
NSC	1.0555
RSC	0.3785

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	0.1363

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	0.2934
AUC	0.4965
CHANCE divergence	0.0949
Elbow Point	0.0000
JS Distance	0.5810
Synthetic AUC	0.5008
Synthetic Elbow Point	0.1703
Synthetic JS Distance	0.2768