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Report generated at 2020-12-04 21:54:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102168414	334658014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100799075	328702336
Mapped(QC-failed)	0	0
% Mapped	98.6600	98.2200
Paired	102168414	334658014
Paired(QC-failed)	0	0
Read1	51084207	167329007
Read1(QC-failed)	0	0
Read2	51084207	167329007
Read2(QC-failed)	0	0
Properly Paired	99845170	320102484
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7300	95.6500
With itself	100263724	326658529
With itself(QC-failed)	0	0
Singletons	535351	2043807
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.6100
Diff. Chroms	245369	620372
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	44420072	141663705
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7458803	1830718
Paired Opt. Dupes	8526	10233
% Dupes/100	0.1679	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44400908	141095473
Distinct Read Pairs	36945418	139340732
One Read Pair	30563398	137631421
Two Read Pairs	5438262	1682298
NRF = Distinct/Total	0.8321	0.9876
PBC1 = OnePair/Distinct	0.8273	0.9877
PBC2 = OnePair/TwoPair	5.6201	81.8116

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	73922538	279665974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73922538	279665974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	73922538	279665974
Paired(QC-failed)	0	0
Read1	36961269	139832987
Read1(QC-failed)	0	0
Read2	36961269	139832987
Read2(QC-failed)	0	0
Properly Paired	73922538	279665974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	73922538	279665974
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	133411
Np	0
N optimal	133411
N conservative	133411
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.	250
Corr. Est. Fragment Len.	0.1929
Phantom Peak	50
Corr. Phantom Peak	0.1858
Argmin. Corr.	1500
Min. Corr.	0.1721
NSC	1.1206
RSC	1.5142

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	0.4192

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	0.1851
AUC	0.4953
CHANCE divergence	0.1335
Elbow Point	0.0000
JS Distance	0.7447
Synthetic AUC	0.5083
Synthetic Elbow Point	0.3600
Synthetic JS Distance	0.4385