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Report generated at 2021-10-10 12:00:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120012148	216279744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104278903	212268741
Mapped(QC-failed)	0	0
% Mapped	86.8900	98.1500
Paired	120012148	216279744
Paired(QC-failed)	0	0
Read1	60006074	108139872
Read1(QC-failed)	0	0
Read2	60006074	108139872
Read2(QC-failed)	0	0
Properly Paired	101648090	208007441
Properly Paired(QC-failed)	0	0
% Properly Paired	84.7000	96.1800
With itself	102407398	210903306
With itself(QC-failed)	0	0
Singletons	1871505	1365435
Singletons(QC-failed)	0	0
% Singleton	1.5600	0.6300
Diff. Chroms	441785	1643621
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	45264140	86702361
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4925309	3631684
Paired Opt. Dupes	11136	20901
% Dupes/100	0.1088	0.0419

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45261762	86645143
Distinct Read Pairs	40336699	83016384
One Read Pair	35868483	79488299
Two Read Pairs	4049378	3431092
NRF = Distinct/Total	0.8912	0.9581
PBC1 = OnePair/Distinct	0.8892	0.9575
PBC2 = OnePair/TwoPair	8.8578	23.1671

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	80677662	166141354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80677662	166141354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80677662	166141354
Paired(QC-failed)	0	0
Read1	40338831	83070677
Read1(QC-failed)	0	0
Read2	40338831	83070677
Read2(QC-failed)	0	0
Properly Paired	80677662	166141354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80677662	166141354
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	41730
Np	0
N optimal	41730
N conservative	41730
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.	205
Corr. Est. Fragment Len.	0.3945
Phantom Peak	55
Corr. Phantom Peak	0.3669
Argmin. Corr.	1500
Min. Corr.	0.1976
NSC	1.9966
RSC	1.1635

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	0.6218

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	0.1143
AUC	0.4944
CHANCE divergence	0.1414
Elbow Point	0.0000
JS Distance	0.9367
Synthetic AUC	0.5002
Synthetic Elbow Point	0.5743
Synthetic JS Distance	0.6206