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Report generated at 2022-01-07 13:29:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	234801308	201652566
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	233240885	198032065
Mapped(QC-failed)	0	0
% Mapped	99.3400	98.2000
Paired	234801308	201652566
Paired(QC-failed)	0	0
Read1	117400654	100826283
Read1(QC-failed)	0	0
Read2	117400654	100826283
Read2(QC-failed)	0	0
Properly Paired	222557623	194936556
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7900	96.6700
With itself	232203811	196867125
With itself(QC-failed)	0	0
Singletons	1037074	1164940
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5800
Diff. Chroms	165571	328067
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	103933298	84633399
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3160403	1125235
Paired Opt. Dupes	1578	1306
% Dupes/100	0.0304	0.0133

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	103920991	84626173
Distinct Read Pairs	100761834	83501515
One Read Pair	97785693	82459535
Two Read Pairs	2812265	999176
NRF = Distinct/Total	0.9696	0.9867
PBC1 = OnePair/Distinct	0.9705	0.9875
PBC2 = OnePair/TwoPair	34.7712	82.5275

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	201545790	167016328
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	201545790	167016328
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	201545790	167016328
Paired(QC-failed)	0	0
Read1	100772895	83508164
Read1(QC-failed)	0	0
Read2	100772895	83508164
Read2(QC-failed)	0	0
Properly Paired	201545790	167016328
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	201545790	167016328
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	291057
Np	0
N optimal	291057
N conservative	291057
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.	135
Corr. Est. Fragment Len.	0.1881
Phantom Peak	55
Corr. Phantom Peak	0.1820
Argmin. Corr.	1500
Min. Corr.	0.1805
NSC	1.0424
RSC	4.9216

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	0.5438

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	0.1516
AUC	0.4971
CHANCE divergence	0.1801
Elbow Point	0.0000
JS Distance	0.6905
Synthetic AUC	0.5028
Synthetic Elbow Point	0.3327
Synthetic JS Distance	0.4955