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Report generated at 2020-05-02 14:25:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56418358	56737366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49003487	53249558
Mapped(QC-failed)	0	0
% Mapped	86.8600	93.8500
Paired	56418358	56737366
Paired(QC-failed)	0	0
Read1	28209179	28368683
Read1(QC-failed)	0	0
Read2	28209179	28368683
Read2(QC-failed)	0	0
Properly Paired	47007139	46970465
Properly Paired(QC-failed)	0	0
% Properly Paired	83.3200	82.7900
With itself	47976996	52253794
With itself(QC-failed)	0	0
Singletons	1026491	995764
Singletons(QC-failed)	0	0
% Singleton	1.8200	1.7600
Diff. Chroms	378087	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	19665715	19151739
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	268799	222856
Paired Opt. Dupes	3322	2619
% Dupes/100	0.0137	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19665004	19151685
Distinct Read Pairs	19396213	18928829
One Read Pair	19130705	18708139
Two Read Pairs	262299	218547
NRF = Distinct/Total	0.9863	0.9884
PBC1 = OnePair/Distinct	0.9863	0.9883
PBC2 = OnePair/TwoPair	72.9347	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	38793832	37857766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38793832	37857766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38793832	37857766
Paired(QC-failed)	0	0
Read1	19396916	18928883
Read1(QC-failed)	0	0
Read2	19396916	18928883
Read2(QC-failed)	0	0
Properly Paired	38793832	37857766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38793832	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	108997
Np	0
N optimal	108997
N conservative	108997
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.	265
Corr. Est. Fragment Len.	0.2024
Phantom Peak	50
Corr. Phantom Peak	0.2168
Argmin. Corr.	1500
Min. Corr.	0.1789
NSC	1.1316
RSC	0.6209

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	0.1685

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	0.1733
AUC	0.4934
CHANCE divergence	0.3358
Elbow Point	0.0000
JS Distance	0.6425
Synthetic AUC	0.5030
Synthetic Elbow Point	0.1048
Synthetic JS Distance	0.3564