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Report generated at 2020-06-10 11:56:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120666182	127861076
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119807624	126069958
Mapped(QC-failed)	0	0
% Mapped	99.2900	98.6000
Paired	120666182	127861076
Paired(QC-failed)	0	0
Read1	60333091	63930538
Read1(QC-failed)	0	0
Read2	60333091	63930538
Read2(QC-failed)	0	0
Properly Paired	119096702	122750247
Properly Paired(QC-failed)	0	0
% Properly Paired	98.7000	96.0000
With itself	119284031	125397302
With itself(QC-failed)	0	0
Singletons	523593	672656
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.5300
Diff. Chroms	32789	127073
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	55504893	54205503
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1640050	466424
Paired Opt. Dupes	4639	4293
% Dupes/100	0.0295	0.0086

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55499236	54190280
Distinct Read Pairs	53859373	53725300
One Read Pair	52326000	53274643
Two Read Pairs	1444048	442720
NRF = Distinct/Total	0.9705	0.9914
PBC1 = OnePair/Distinct	0.9715	0.9916
PBC2 = OnePair/TwoPair	36.2356	120.3348

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	107729686	107478158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107729686	107478158
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107729686	107478158
Paired(QC-failed)	0	0
Read1	53864843	53739079
Read1(QC-failed)	0	0
Read2	53864843	53739079
Read2(QC-failed)	0	0
Properly Paired	107729686	107478158
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107729686	107478158
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	140138
Np	0
N optimal	140138
N conservative	140138
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.	0.2190
Phantom Peak	45
Corr. Phantom Peak	0.1964
Argmin. Corr.	1500
Min. Corr.	0.1827
NSC	1.1987
RSC	2.6378

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	0.6019

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	0.1240
AUC	0.4961
CHANCE divergence	0.1411
Elbow Point	0.0000
JS Distance	0.8340
Synthetic AUC	0.4976
Synthetic Elbow Point	0.4418
Synthetic JS Distance	0.5592