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Report generated at 2020-07-10 12:29:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102114754	104183442
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100259769	101561725
Mapped(QC-failed)	0	0
% Mapped	98.1800	97.4800
Paired	102114754	104183442
Paired(QC-failed)	0	0
Read1	51057377	52091721
Read1(QC-failed)	0	0
Read2	51057377	52091721
Read2(QC-failed)	0	0
Properly Paired	74878611	83193856
Properly Paired(QC-failed)	0	0
% Properly Paired	73.3300	79.8500
With itself	98929274	100020683
With itself(QC-failed)	0	0
Singletons	1330495	1541042
Singletons(QC-failed)	0	0
% Singleton	1.3000	1.4800
Diff. Chroms	20825988	13877524
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	34326685	36259719
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	573625	570314
Paired Opt. Dupes	2595	2544
% Dupes/100	0.0167	0.0157

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34306792	36250789
Distinct Read Pairs	33734772	35680935
One Read Pair	33173581	35127299
Two Read Pairs	550974	542681
NRF = Distinct/Total	0.9833	0.9843
PBC1 = OnePair/Distinct	0.9834	0.9845
PBC2 = OnePair/TwoPair	60.2090	64.7292

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	67506120	71378810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67506120	71378810
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67506120	71378810
Paired(QC-failed)	0	0
Read1	33753060	35689405
Read1(QC-failed)	0	0
Read2	33753060	35689405
Read2(QC-failed)	0	0
Properly Paired	67506120	71378810
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67506120	71378810
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	220103
Np	0
N optimal	220103
N conservative	220103
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.	125
Corr. Est. Fragment Len.	0.1749
Phantom Peak	55
Corr. Phantom Peak	0.1746
Argmin. Corr.	1500
Min. Corr.	0.1710
NSC	1.0227
RSC	1.0909

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	0.2355

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	0.2333
AUC	0.4951
CHANCE divergence	0.1224
Elbow Point	0.0000
JS Distance	0.6715
Synthetic AUC	0.4983
Synthetic Elbow Point	0.1684
Synthetic JS Distance	0.3455