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Report generated at 2021-10-22 22:16:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	253738550	168628396
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	177589711	163343908
Mapped(QC-failed)	0	0
% Mapped	69.9900	96.8700
Paired	253738550	168628396
Paired(QC-failed)	0	0
Read1	126869275	84314198
Read1(QC-failed)	0	0
Read2	126869275	84314198
Read2(QC-failed)	0	0
Properly Paired	175834694	159133434
Properly Paired(QC-failed)	0	0
% Properly Paired	69.3000	94.3700
With itself	176423408	162244869
With itself(QC-failed)	0	0
Singletons	1166303	1099039
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.6500
Diff. Chroms	272611	2067566
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	77601820	66322288
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	42345962	4095947
Paired Opt. Dupes	40023	41316
% Dupes/100	0.5457	0.0618

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	77599907	66307420
Distinct Read Pairs	35254974	62212428
One Read Pair	14194368	58305094
Two Read Pairs	9768026	3728896
NRF = Distinct/Total	0.4543	0.9382
PBC1 = OnePair/Distinct	0.4026	0.9372
PBC2 = OnePair/TwoPair	1.4531	15.6360

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	70511716	124452682
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70511716	124452682
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70511716	124452682
Paired(QC-failed)	0	0
Read1	35255858	62226341
Read1(QC-failed)	0	0
Read2	35255858	62226341
Read2(QC-failed)	0	0
Properly Paired	70511716	124452682
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70511716	124452682
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	71336
Np	0
N optimal	71336
N conservative	71336
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.	185
Corr. Est. Fragment Len.	0.2576
Phantom Peak	55
Corr. Phantom Peak	0.2391
Argmin. Corr.	1500
Min. Corr.	0.1653
NSC	1.5590
RSC	1.2510

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	0.4659

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	0.1494
AUC	0.4941
CHANCE divergence	0.1482
Elbow Point	0.0000
JS Distance	0.8180
Synthetic AUC	0.5004
Synthetic Elbow Point	0.4407
Synthetic JS Distance	0.5168