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Report generated at 2020-05-02 15:04:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71920274	56737366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67572794	53249558
Mapped(QC-failed)	0	0
% Mapped	93.9600	93.8500
Paired	71920274	56737366
Paired(QC-failed)	0	0
Read1	35960137	28368683
Read1(QC-failed)	0	0
Read2	35960137	28368683
Read2(QC-failed)	0	0
Properly Paired	66226534	46970465
Properly Paired(QC-failed)	0	0
% Properly Paired	92.0800	82.7900
With itself	66898804	52253794
With itself(QC-failed)	0	0
Singletons	673990	995764
Singletons(QC-failed)	0	0
% Singleton	0.9400	1.7600
Diff. Chroms	399713	3675402
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	29607610	19151739
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	303343	222856
Paired Opt. Dupes	4724	2619
% Dupes/100	0.0102	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29606904	19151685
Distinct Read Pairs	29303571	18928829
One Read Pair	29002864	18708139
Two Read Pairs	298108	218547
NRF = Distinct/Total	0.9898	0.9884
PBC1 = OnePair/Distinct	0.9897	0.9883
PBC2 = OnePair/TwoPair	97.2898	85.6024

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	58608534	37857766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58608534	37857766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58608534	37857766
Paired(QC-failed)	0	0
Read1	29304267	18928883
Read1(QC-failed)	0	0
Read2	29304267	18928883
Read2(QC-failed)	0	0
Properly Paired	58608534	37857766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58608534	37857766
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	149193
Np	0
N optimal	149193
N conservative	149193
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.	270
Corr. Est. Fragment Len.	0.2095
Phantom Peak	50
Corr. Phantom Peak	0.2051
Argmin. Corr.	1500
Min. Corr.	0.1915
NSC	1.0939
RSC	1.3220

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	0.3742

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	0.1339
AUC	0.4947
CHANCE divergence	0.3253
Elbow Point	0.0000
JS Distance	0.7356
Synthetic AUC	0.5038
Synthetic Elbow Point	0.1665
Synthetic JS Distance	0.4581