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Report generated at 2020-05-02 12:06:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52077040	45100544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46199644	42784977
Mapped(QC-failed)	0	0
% Mapped	88.7100	94.8700
Paired	52077040	45100544
Paired(QC-failed)	0	0
Read1	26038520	22550272
Read1(QC-failed)	0	0
Read2	26038520	22550272
Read2(QC-failed)	0	0
Properly Paired	43656063	34886479
Properly Paired(QC-failed)	0	0
% Properly Paired	83.8300	77.3500
With itself	45093470	41495730
With itself(QC-failed)	0	0
Singletons	1106174	1289247
Singletons(QC-failed)	0	0
% Singleton	2.1200	2.8600
Diff. Chroms	676003	4523333
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	17448941	13208684
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	545864	154251
Paired Opt. Dupes	2651	1783
% Dupes/100	0.0313	0.0117

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17448732	13208667
Distinct Read Pairs	16902879	13054416
One Read Pair	16371257	12901708
Two Read Pairs	517707	151186
NRF = Distinct/Total	0.9687	0.9883
PBC1 = OnePair/Distinct	0.9685	0.9883
PBC2 = OnePair/TwoPair	31.6226	85.3367

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	33806154	26108866
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33806154	26108866
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	33806154	26108866
Paired(QC-failed)	0	0
Read1	16903077	13054433
Read1(QC-failed)	0	0
Read2	16903077	13054433
Read2(QC-failed)	0	0
Properly Paired	33806154	26108866
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	33806154	26108866
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	139656
Np	0
N optimal	139656
N conservative	139656
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.	250
Corr. Est. Fragment Len.	0.2517
Phantom Peak	50
Corr. Phantom Peak	0.2490
Argmin. Corr.	1500
Min. Corr.	0.2035
NSC	1.2365
RSC	1.0589

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	0.3582

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	0.0971
AUC	0.4930
CHANCE divergence	0.5131
Elbow Point	0.0000
JS Distance	0.7491
Synthetic AUC	0.4938
Synthetic Elbow Point	0.1507
Synthetic JS Distance	0.4519