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Report generated at 2021-03-18 18:42:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	22750482	120326326
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	22135573	115169165
Mapped(QC-failed)	0	0
% Mapped	97.3000	95.7100
Paired	22750482	120326326
Paired(QC-failed)	0	0
Read1	11375241	60163163
Read1(QC-failed)	0	0
Read2	11375241	60163163
Read2(QC-failed)	0	0
Properly Paired	20955667	99959048
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1100	83.0700
With itself	21971797	113514451
With itself(QC-failed)	0	0
Singletons	163776	1654714
Singletons(QC-failed)	0	0
% Singleton	0.7200	1.3800
Diff. Chroms	698216	8596702
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	9347974	44206103
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	88309	461681
Paired Opt. Dupes	824	1289
% Dupes/100	0.0094	0.0104

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	9331329	44178985
Distinct Read Pairs	9243775	43721013
One Read Pair	9157219	43278165
Two Read Pairs	85661	434626
NRF = Distinct/Total	0.9906	0.9896
PBC1 = OnePair/Distinct	0.9906	0.9899
PBC2 = OnePair/TwoPair	106.9007	99.5756

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	18519330	87488844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	18519330	87488844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	18519330	87488844
Paired(QC-failed)	0	0
Read1	9259665	43744422
Read1(QC-failed)	0	0
Read2	9259665	43744422
Read2(QC-failed)	0	0
Properly Paired	18519330	87488844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	18519330	87488844
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	52253
Np	0
N optimal	52253
N conservative	52253
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 (11M)

	rep1
Reads	11139443
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.1393
Phantom Peak	50
Corr. Phantom Peak	0.1408
Argmin. Corr.	1500
Min. Corr.	0.1313
NSC	1.0613
RSC	0.8482

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	0.1256

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	0.2179
AUC	0.4906
CHANCE divergence	0.2415
Elbow Point	0.0000
JS Distance	0.6013
Synthetic AUC	0.5082
Synthetic Elbow Point	0.1640
Synthetic JS Distance	0.3088