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Report generated at 2021-01-20 05:45:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	153285862	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107415255	187969057
Mapped(QC-failed)	0	0
% Mapped	70.0800	97.0900
Paired	153285862	193594802
Paired(QC-failed)	0	0
Read1	76642931	96797401
Read1(QC-failed)	0	0
Read2	76642931	96797401
Read2(QC-failed)	0	0
Properly Paired	105728208	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	68.9700	95.1900
With itself	106953534	185784698
With itself(QC-failed)	0	0
Singletons	461721	2184359
Singletons(QC-failed)	0	0
% Singleton	0.3000	1.1300
Diff. Chroms	133387	610670
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	48473242	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7946172	539110
Paired Opt. Dupes	11919	19807
% Dupes/100	0.1639	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48241010	77646644
Distinct Read Pairs	40341142	77172156
One Read Pair	33635692	76701136
Two Read Pairs	5677758	467668
NRF = Distinct/Total	0.8362	0.9939
PBC1 = OnePair/Distinct	0.8338	0.9939
PBC2 = OnePair/TwoPair	5.9241	164.0077

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	81054140	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81054140	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	81054140	155345422
Paired(QC-failed)	0	0
Read1	40527070	77672711
Read1(QC-failed)	0	0
Read2	40527070	77672711
Read2(QC-failed)	0	0
Properly Paired	81054140	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	81054140	155345422
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	123215
Np	0
N optimal	123215
N conservative	123215
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.	145
Corr. Est. Fragment Len.	0.2032
Phantom Peak	50
Corr. Phantom Peak	0.1970
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.1947
RSC	1.2283

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	0.3169

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	0.2181
AUC	0.4955
CHANCE divergence	0.1109
Elbow Point	0.0000
JS Distance	0.7282
Synthetic AUC	0.5084
Synthetic Elbow Point	0.2911
Synthetic JS Distance	0.3966