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Report generated at 2020-04-10 02:04:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	49627446	163266420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46849109	147055862
Mapped(QC-failed)	0	0
% Mapped	94.4000	90.0700
Paired	49627446	163266420
Paired(QC-failed)	0	0
Read1	24813723	81633210
Read1(QC-failed)	0	0
Read2	24813723	81633210
Read2(QC-failed)	0	0
Properly Paired	45559052	131717614
Properly Paired(QC-failed)	0	0
% Properly Paired	91.8000	80.6800
With itself	45855816	140493174
With itself(QC-failed)	0	0
Singletons	993293	6562688
Singletons(QC-failed)	0	0
% Singleton	2.0000	4.0200
Diff. Chroms	43932	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	20804346	43256772
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17555918	4012335
Paired Opt. Dupes	560785	298855
% Dupes/100	0.8439	0.0928

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	20803203	42734600
Distinct Read Pairs	3248271	38829854
One Read Pair	438624	35276734
Two Read Pairs	319377	3232143
NRF = Distinct/Total	0.1561	0.9086
PBC1 = OnePair/Distinct	0.1350	0.9085
PBC2 = OnePair/TwoPair	1.3734	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	6496856	78488874
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	6496856	78488874
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	6496856	78488874
Paired(QC-failed)	0	0
Read1	3248428	39244437
Read1(QC-failed)	0	0
Read2	3248428	39244437
Read2(QC-failed)	0	0
Properly Paired	6496856	78488874
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	6496856	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	67248
Np	0
N optimal	67248
N conservative	67248
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.	135
Corr. Est. Fragment Len.	0.0673
Phantom Peak	55
Corr. Phantom Peak	0.0497
Argmin. Corr.	1500
Min. Corr.	0.0433
NSC	1.5551
RSC	3.7592

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	0.2616

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	0.0910
AUC	0.4841
CHANCE divergence	0.6585
Elbow Point	0.0000
JS Distance	0.7241
Synthetic AUC	0.5007
Synthetic Elbow Point	0.2383
Synthetic JS Distance	0.3342