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Report generated at 2022-01-13 08:44:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	48280700	52208364
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45253974	46961269
Mapped(QC-failed)	0	0
% Mapped	93.7300	89.9500
Paired	48280700	52208364
Paired(QC-failed)	0	0
Read1	24140350	26104182
Read1(QC-failed)	0	0
Read2	24140350	26104182
Read2(QC-failed)	0	0
Properly Paired	44133850	38339710
Properly Paired(QC-failed)	0	0
% Properly Paired	91.4100	73.4400
With itself	44599003	44775897
With itself(QC-failed)	0	0
Singletons	654971	2185372
Singletons(QC-failed)	0	0
% Singleton	1.3600	4.1900
Diff. Chroms	317877	4612399
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	19721299	13624196
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	192297	312822
Paired Opt. Dupes	4853	3040
% Dupes/100	0.0098	0.0230

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19719240	13619156
Distinct Read Pairs	19526957	13306524
One Read Pair	19336277	13000280
Two Read Pairs	189091	300008
NRF = Distinct/Total	0.9902	0.9770
PBC1 = OnePair/Distinct	0.9902	0.9770
PBC2 = OnePair/TwoPair	102.2591	43.3331

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	39058004	26622748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39058004	26622748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	39058004	26622748
Paired(QC-failed)	0	0
Read1	19529002	13311374
Read1(QC-failed)	0	0
Read2	19529002	13311374
Read2(QC-failed)	0	0
Properly Paired	39058004	26622748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	39058004	26622748
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	152128
Np	0
N optimal	152128
N conservative	152128
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.	240
Corr. Est. Fragment Len.	0.2206
Phantom Peak	50
Corr. Phantom Peak	0.2166
Argmin. Corr.	1500
Min. Corr.	0.2061
NSC	1.0702
RSC	1.3814

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	0.4871

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	0.0974
AUC	0.4935
CHANCE divergence	0.3784
Elbow Point	0.0000
JS Distance	0.8161
Synthetic AUC	0.5073
Synthetic Elbow Point	0.2132
Synthetic JS Distance	0.5261