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Report generated at 2020-07-15 11:14:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171666024	137918120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	164578567	134017183
Mapped(QC-failed)	0	0
% Mapped	95.8700	97.1700
Paired	171666024	137918120
Paired(QC-failed)	0	0
Read1	85833012	68959060
Read1(QC-failed)	0	0
Read2	85833012	68959060
Read2(QC-failed)	0	0
Properly Paired	161901882	131780533
Properly Paired(QC-failed)	0	0
% Properly Paired	94.3100	95.5500
With itself	163460549	133321503
With itself(QC-failed)	0	0
Singletons	1118018	695680
Singletons(QC-failed)	0	0
% Singleton	0.6500	0.5000
Diff. Chroms	812456	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	69628340	57429716
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	400683	221431
Paired Opt. Dupes	3405	1055
% Dupes/100	0.0058	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	69622203	57381501
Distinct Read Pairs	69221552	57160737
One Read Pair	68824113	56941613
Two Read Pairs	394329	217603
NRF = Distinct/Total	0.9942	0.9962
PBC1 = OnePair/Distinct	0.9943	0.9962
PBC2 = OnePair/TwoPair	174.5347	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	138455314	114416570
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	138455314	114416570
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	138455314	114416570
Paired(QC-failed)	0	0
Read1	69227657	57208285
Read1(QC-failed)	0	0
Read2	69227657	57208285
Read2(QC-failed)	0	0
Properly Paired	138455314	114416570
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	138455314	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	137156
Np	0
N optimal	137156
N conservative	137156
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.	105
Corr. Est. Fragment Len.	0.1836
Phantom Peak	50
Corr. Phantom Peak	0.2031
Argmin. Corr.	1500
Min. Corr.	0.1765
NSC	1.0405
RSC	0.2685

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	0.0881

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	0.2841
AUC	0.4965
CHANCE divergence	0.0985
Elbow Point	0.0000
JS Distance	0.5925
Synthetic AUC	0.4968
Synthetic Elbow Point	0.0916
Synthetic JS Distance	0.2762