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Report generated at 2020-04-08 09:04:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	67082466	67922260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65801929	66671924
Mapped(QC-failed)	0	0
% Mapped	98.0900	98.1600
Paired	67082466	67922260
Paired(QC-failed)	0	0
Read1	33541233	33961130
Read1(QC-failed)	0	0
Read2	33541233	33961130
Read2(QC-failed)	0	0
Properly Paired	65029227	65974861
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9400	97.1300
With itself	65250993	66190036
With itself(QC-failed)	0	0
Singletons	550936	481888
Singletons(QC-failed)	0	0
% Singleton	0.8200	0.7100
Diff. Chroms	68943	48289
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	29544683	29193042
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16244308	5293802
Paired Opt. Dupes	2258	2781
% Dupes/100	0.5498	0.1813

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29544047	29163692
Distinct Read Pairs	13299975	23873561
One Read Pair	7235771	19715715
Two Read Pairs	2532760	3278552
NRF = Distinct/Total	0.4502	0.8186
PBC1 = OnePair/Distinct	0.5440	0.8258
PBC2 = OnePair/TwoPair	2.8569	6.0135

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	26600750	47798480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	26600750	47798480
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	26600750	47798480
Paired(QC-failed)	0	0
Read1	13300375	23899240
Read1(QC-failed)	0	0
Read2	13300375	23899240
Read2(QC-failed)	0	0
Properly Paired	26600750	47798480
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	26600750	47798480
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	70693
Np	0
N optimal	70693
N conservative	70693
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.	0.1262
Phantom Peak	50
Corr. Phantom Peak	0.1124
Argmin. Corr.	1500
Min. Corr.	0.1025
NSC	1.2305
RSC	2.4037

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	0.1533

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	0.2214
AUC	0.4921
CHANCE divergence	0.2089
Elbow Point	0.0000
JS Distance	0.6465
Synthetic AUC	0.5084
Synthetic Elbow Point	0.1409
Synthetic JS Distance	0.3266