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Report generated at 2020-07-14 19:10:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52254732	143118944
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48786920	139990469
Mapped(QC-failed)	0	0
% Mapped	93.3600	97.8100
Paired	52254732	143118944
Paired(QC-failed)	0	0
Read1	26127366	71559472
Read1(QC-failed)	0	0
Read2	26127366	71559472
Read2(QC-failed)	0	0
Properly Paired	48213586	137871752
Properly Paired(QC-failed)	0	0
% Properly Paired	92.2700	96.3300
With itself	48484647	139333057
With itself(QC-failed)	0	0
Singletons	302273	657412
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.4600
Diff. Chroms	116522	791653
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	21433018	60254678
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	118285	215954
Paired Opt. Dupes	4094	979
% Dupes/100	0.0055	0.0036

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21430353	60210805
Distinct Read Pairs	21312088	59995465
One Read Pair	21194379	59781108
Two Read Pairs	117156	213413
NRF = Distinct/Total	0.9945	0.9964
PBC1 = OnePair/Distinct	0.9945	0.9964
PBC2 = OnePair/TwoPair	180.9073	280.1193

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	42629466	120077448
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42629466	120077448
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42629466	120077448
Paired(QC-failed)	0	0
Read1	21314733	60038724
Read1(QC-failed)	0	0
Read2	21314733	60038724
Read2(QC-failed)	0	0
Properly Paired	42629466	120077448
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42629466	120077448
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	40733
Np	0
N optimal	40733
N conservative	40733
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.	145
Corr. Est. Fragment Len.	0.2205
Phantom Peak	50
Corr. Phantom Peak	0.2312
Argmin. Corr.	1500
Min. Corr.	0.1779
NSC	1.2390
RSC	0.7992

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	0.2481

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	0.2203
AUC	0.4938
CHANCE divergence	0.1390
Elbow Point	0.0000
JS Distance	0.6781
Synthetic AUC	0.5041
Synthetic Elbow Point	0.2848
Synthetic JS Distance	0.3895