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Report generated at 2020-07-15 09:32:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	178827422	137918120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	172038123	134017183
Mapped(QC-failed)	0	0
% Mapped	96.2000	97.1700
Paired	178827422	137918120
Paired(QC-failed)	0	0
Read1	89413711	68959060
Read1(QC-failed)	0	0
Read2	89413711	68959060
Read2(QC-failed)	0	0
Properly Paired	169397970	131780533
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7300	95.5500
With itself	171104186	133321503
With itself(QC-failed)	0	0
Singletons	933937	695680
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5000
Diff. Chroms	1011970	866285
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	74628903	57429716
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	419316	221431
Paired Opt. Dupes	2061	1055
% Dupes/100	0.0056	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	74621692	57381501
Distinct Read Pairs	74202426	57160737
One Read Pair	73786096	56941613
Two Read Pairs	413452	217603
NRF = Distinct/Total	0.9944	0.9962
PBC1 = OnePair/Distinct	0.9944	0.9962
PBC2 = OnePair/TwoPair	178.4635	261.6766

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	148419174	114416570
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	148419174	114416570
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	148419174	114416570
Paired(QC-failed)	0	0
Read1	74209587	57208285
Read1(QC-failed)	0	0
Read2	74209587	57208285
Read2(QC-failed)	0	0
Properly Paired	148419174	114416570
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	148419174	114416570
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	226669
Np	0
N optimal	226669
N conservative	226669
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.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.2038
Argmin. Corr.	1500
Min. Corr.	0.1808
NSC	1.0458
RSC	0.3596

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	0.3234

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	0.2401
AUC	0.4967
CHANCE divergence	0.0996
Elbow Point	0.0000
JS Distance	0.7175
Synthetic AUC	0.5026
Synthetic Elbow Point	0.1994
Synthetic JS Distance	0.3542