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Report generated at 2020-07-15 01:07:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79833186	168466658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76639896	164624745
Mapped(QC-failed)	0	0
% Mapped	96.0000	97.7200
Paired	79833186	168466658
Paired(QC-failed)	0	0
Read1	39916593	84233329
Read1(QC-failed)	0	0
Read2	39916593	84233329
Read2(QC-failed)	0	0
Properly Paired	75884649	162184899
Properly Paired(QC-failed)	0	0
% Properly Paired	95.0500	96.2700
With itself	76298199	163825228
With itself(QC-failed)	0	0
Singletons	341697	799517
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.4700
Diff. Chroms	222161	775348
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	34319360	70866487
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	446945	312564
Paired Opt. Dupes	7128	1254
% Dupes/100	0.0130	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34311423	70787609
Distinct Read Pairs	33864611	70476699
One Read Pair	33423585	70167382
Two Read Pairs	435312	307768
NRF = Distinct/Total	0.9870	0.9956
PBC1 = OnePair/Distinct	0.9870	0.9956
PBC2 = OnePair/TwoPair	76.7808	227.9879

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	67744830	141107846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67744830	141107846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67744830	141107846
Paired(QC-failed)	0	0
Read1	33872415	70553923
Read1(QC-failed)	0	0
Read2	33872415	70553923
Read2(QC-failed)	0	0
Properly Paired	67744830	141107846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67744830	141107846
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	39790
Np	0
N optimal	39790
N conservative	39790
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.	200
Corr. Est. Fragment Len.	0.2815
Phantom Peak	50
Corr. Phantom Peak	0.2734
Argmin. Corr.	1500
Min. Corr.	0.1873
NSC	1.5034
RSC	1.0946

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	0.4002

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	0.1864
AUC	0.4951
CHANCE divergence	0.1192
Elbow Point	0.0000
JS Distance	0.8046
Synthetic AUC	0.4954
Synthetic Elbow Point	0.3880
Synthetic JS Distance	0.4769