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Report generated at 2020-06-05 17:46:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100977754	103045968
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94591289	98644908
Mapped(QC-failed)	0	0
% Mapped	93.6800	95.7300
Paired	100977754	103045968
Paired(QC-failed)	0	0
Read1	50488877	51522984
Read1(QC-failed)	0	0
Read2	50488877	51522984
Read2(QC-failed)	0	0
Properly Paired	88334927	94442886
Properly Paired(QC-failed)	0	0
% Properly Paired	87.4800	91.6500
With itself	89041132	95330195
With itself(QC-failed)	0	0
Singletons	5550157	3314713
Singletons(QC-failed)	0	0
% Singleton	5.5000	3.2200
Diff. Chroms	400761	525331
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	36930242	40142877
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3586735	1418251
Paired Opt. Dupes	3411	4354
% Dupes/100	0.0971	0.0353

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36929536	40111338
Distinct Read Pairs	33342864	38694462
One Read Pair	30104709	37332587
Two Read Pairs	2922542	1311871
NRF = Distinct/Total	0.9029	0.9647
PBC1 = OnePair/Distinct	0.9029	0.9648
PBC2 = OnePair/TwoPair	10.3009	28.4575

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	66687014	77449252
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66687014	77449252
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66687014	77449252
Paired(QC-failed)	0	0
Read1	33343507	38724626
Read1(QC-failed)	0	0
Read2	33343507	38724626
Read2(QC-failed)	0	0
Properly Paired	66687014	77449252
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66687014	77449252
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	152922
Np	0
N optimal	152922
N conservative	152922
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.	130
Corr. Est. Fragment Len.	0.1710
Phantom Peak	50
Corr. Phantom Peak	0.1772
Argmin. Corr.	1500
Min. Corr.	0.1681
NSC	1.0177
RSC	0.3275

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	0.2499

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	0.2439
AUC	0.4950
CHANCE divergence	0.1154
Elbow Point	0.0000
JS Distance	0.6824
Synthetic AUC	0.4956
Synthetic Elbow Point	0.1796
Synthetic JS Distance	0.3340