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Report generated at 2020-06-05 11:58:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	66460248	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53616384	86768460
Mapped(QC-failed)	0	0
% Mapped	80.6700	97.7100
Paired	66460248	88801120
Paired(QC-failed)	0	0
Read1	33230124	44400560
Read1(QC-failed)	0	0
Read2	33230124	44400560
Read2(QC-failed)	0	0
Properly Paired	52392513	85806342
Properly Paired(QC-failed)	0	0
% Properly Paired	78.8300	96.6300
With itself	53061557	86430737
With itself(QC-failed)	0	0
Singletons	554827	337723
Singletons(QC-failed)	0	0
% Singleton	0.8300	0.3800
Diff. Chroms	96385	102733
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	20845099	37887648
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11951784	723067
Paired Opt. Dupes	1806	3740
% Dupes/100	0.5734	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	20842068	37657559
Distinct Read Pairs	8892015	36953662
One Read Pair	4156018	36265990
Two Read Pairs	1830096	673657
NRF = Distinct/Total	0.4266	0.9813
PBC1 = OnePair/Distinct	0.4674	0.9814
PBC2 = OnePair/TwoPair	2.2709	53.8345

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	17786630	74329162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	17786630	74329162
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	17786630	74329162
Paired(QC-failed)	0	0
Read1	8893315	37164581
Read1(QC-failed)	0	0
Read2	8893315	37164581
Read2(QC-failed)	0	0
Properly Paired	17786630	74329162
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	17786630	74329162
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	75054
Np	0
N optimal	75054
N conservative	75054
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.	125
Corr. Est. Fragment Len.	0.1412
Phantom Peak	50
Corr. Phantom Peak	0.1650
Argmin. Corr.	1500
Min. Corr.	0.1232
NSC	1.1458
RSC	0.4301

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	0.0534

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	0.2188
AUC	0.4903
CHANCE divergence	0.2870
Elbow Point	0.0000
JS Distance	0.6067
Synthetic AUC	0.5044
Synthetic Elbow Point	0.1063
Synthetic JS Distance	0.2740