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Report generated at 2020-04-10 01:08:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	42791642	163266420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40881883	147055862
Mapped(QC-failed)	0	0
% Mapped	95.5400	90.0700
Paired	42791642	163266420
Paired(QC-failed)	0	0
Read1	21395821	81633210
Read1(QC-failed)	0	0
Read2	21395821	81633210
Read2(QC-failed)	0	0
Properly Paired	40158010	131717614
Properly Paired(QC-failed)	0	0
% Properly Paired	93.8500	80.6800
With itself	40510424	140493174
With itself(QC-failed)	0	0
Singletons	371459	6562688
Singletons(QC-failed)	0	0
% Singleton	0.8700	4.0200
Diff. Chroms	28096	2800249
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	18035323	43256772
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13388901	4012335
Paired Opt. Dupes	152413	298855
% Dupes/100	0.7424	0.0928

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	18033313	42734600
Distinct Read Pairs	4645909	38829854
One Read Pair	1010169	35276734
Two Read Pairs	854405	3232143
NRF = Distinct/Total	0.2576	0.9086
PBC1 = OnePair/Distinct	0.2174	0.9085
PBC2 = OnePair/TwoPair	1.1823	10.9143

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	9292844	78488874
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	9292844	78488874
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	9292844	78488874
Paired(QC-failed)	0	0
Read1	4646422	39244437
Read1(QC-failed)	0	0
Read2	4646422	39244437
Read2(QC-failed)	0	0
Properly Paired	9292844	78488874
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	9292844	78488874
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	39317
Np	0
N optimal	39317
N conservative	39317
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.	150
Corr. Est. Fragment Len.	0.1839
Phantom Peak	50
Corr. Phantom Peak	0.1542
Argmin. Corr.	1500
Min. Corr.	0.0857
NSC	2.1462
RSC	1.4324

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	0.6507

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	0.0387
AUC	0.4867
CHANCE divergence	0.7223
Elbow Point	0.0000
JS Distance	0.8088
Synthetic AUC	0.5159
Synthetic Elbow Point	0.5211
Synthetic JS Distance	0.5869