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Report generated at 2020-07-08 06:50:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	183413056	208397864
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	182252753	205001727
Mapped(QC-failed)	0	0
% Mapped	99.3700	98.3700
Paired	183413056	208397864
Paired(QC-failed)	0	0
Read1	91706528	104198932
Read1(QC-failed)	0	0
Read2	91706528	104198932
Read2(QC-failed)	0	0
Properly Paired	181283322	199305736
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8400	95.6400
With itself	181729688	203636968
With itself(QC-failed)	0	0
Singletons	523065	1364759
Singletons(QC-failed)	0	0
% Singleton	0.2900	0.6500
Diff. Chroms	44316	299296
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	85062435	87961350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9747415	1539702
Paired Opt. Dupes	4286	2336
% Dupes/100	0.1146	0.0175

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	85052319	87956751
Distinct Read Pairs	75306270	86417421
One Read Pair	66520219	84991112
Two Read Pairs	7927862	1357061
NRF = Distinct/Total	0.8854	0.9825
PBC1 = OnePair/Distinct	0.8833	0.9835
PBC2 = OnePair/TwoPair	8.3907	62.6288

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	150630040	172843296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	150630040	172843296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	150630040	172843296
Paired(QC-failed)	0	0
Read1	75315020	86421648
Read1(QC-failed)	0	0
Read2	75315020	86421648
Read2(QC-failed)	0	0
Properly Paired	150630040	172843296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	150630040	172843296
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	224655
Np	0
N optimal	224655
N conservative	224655
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.	0.1928
Phantom Peak	55
Corr. Phantom Peak	0.1837
Argmin. Corr.	1500
Min. Corr.	0.1696
NSC	1.1366
RSC	1.6469

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	0.5634

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	0.1642
AUC	0.4967
CHANCE divergence	0.1089
Elbow Point	0.0000
JS Distance	0.7878
Synthetic AUC	0.5028
Synthetic Elbow Point	0.3574
Synthetic JS Distance	0.4855