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Report generated at 2022-01-13 17:16:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61084304	61483794
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53422168	53537979
Mapped(QC-failed)	0	0
% Mapped	87.4600	87.0800
Paired	61084304	61483794
Paired(QC-failed)	0	0
Read1	30542152	30741897
Read1(QC-failed)	0	0
Read2	30542152	30741897
Read2(QC-failed)	0	0
Properly Paired	47770080	45512545
Properly Paired(QC-failed)	0	0
% Properly Paired	78.2000	74.0200
With itself	50866763	48321091
With itself(QC-failed)	0	0
Singletons	2555405	5216888
Singletons(QC-failed)	0	0
% Singleton	4.1800	8.4800
Diff. Chroms	2017465	1709831
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	17774296	7051123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	306840	302597
Paired Opt. Dupes	2588	868
% Dupes/100	0.0173	0.0429

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17774188	7050084
Distinct Read Pairs	17467350	6747724
One Read Pair	17165297	6457557
Two Read Pairs	297346	279052
NRF = Distinct/Total	0.9827	0.9571
PBC1 = OnePair/Distinct	0.9827	0.9570
PBC2 = OnePair/TwoPair	57.7284	23.1411

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	34934912	13497052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34934912	13497052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	34934912	13497052
Paired(QC-failed)	0	0
Read1	17467456	6748526
Read1(QC-failed)	0	0
Read2	17467456	6748526
Read2(QC-failed)	0	0
Properly Paired	34934912	13497052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	34934912	13497052
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	83643
Np	0
N optimal	83643
N conservative	83643
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.	260
Corr. Est. Fragment Len.	0.2019
Phantom Peak	50
Corr. Phantom Peak	0.2160
Argmin. Corr.	1500
Min. Corr.	0.1845
NSC	1.0940
RSC	0.5507

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	0.1576

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	0.1459
AUC	0.4930
CHANCE divergence	0.3206
Elbow Point	0.0000
JS Distance	0.7173
Synthetic AUC	0.4957
Synthetic Elbow Point	0.1098
Synthetic JS Distance	0.4234