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Report generated at 2021-03-22 11:37:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	184068938	120326326
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129350878	115169165
Mapped(QC-failed)	0	0
% Mapped	70.2700	95.7100
Paired	184068938	120326326
Paired(QC-failed)	0	0
Read1	92034469	60163163
Read1(QC-failed)	0	0
Read2	92034469	60163163
Read2(QC-failed)	0	0
Properly Paired	96773993	99959048
Properly Paired(QC-failed)	0	0
% Properly Paired	52.5700	83.0700
With itself	125534368	113514451
With itself(QC-failed)	0	0
Singletons	3816510	1654714
Singletons(QC-failed)	0	0
% Singleton	2.0700	1.3800
Diff. Chroms	2171317	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	44905941	44206103
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2554360	461681
Paired Opt. Dupes	2747	1289
% Dupes/100	0.0569	0.0104

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44903543	44178985
Distinct Read Pairs	42349354	43721013
One Read Pair	39959930	43278165
Two Read Pairs	2244582	434626
NRF = Distinct/Total	0.9431	0.9896
PBC1 = OnePair/Distinct	0.9436	0.9899
PBC2 = OnePair/TwoPair	17.8028	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	84703162	87488844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84703162	87488844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84703162	87488844
Paired(QC-failed)	0	0
Read1	42351581	43744422
Read1(QC-failed)	0	0
Read2	42351581	43744422
Read2(QC-failed)	0	0
Properly Paired	84703162	87488844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84703162	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	254566
Np	0
N optimal	254566
N conservative	254566
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.	145
Corr. Est. Fragment Len.	0.1792
Phantom Peak	55
Corr. Phantom Peak	0.1748
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.0453
RSC	2.3420

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	0.3596

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	0.1905
AUC	0.4966
CHANCE divergence	0.1940
Elbow Point	0.0000
JS Distance	0.6692
Synthetic AUC	0.5030
Synthetic Elbow Point	0.2282
Synthetic JS Distance	0.3999