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Report generated at 2020-05-22 13:14:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61316018	101616908
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57552297	98299386
Mapped(QC-failed)	0	0
% Mapped	93.8600	96.7400
Paired	61316018	101616908
Paired(QC-failed)	0	0
Read1	30658009	50808454
Read1(QC-failed)	0	0
Read2	30658009	50808454
Read2(QC-failed)	0	0
Properly Paired	56460494	95630320
Properly Paired(QC-failed)	0	0
% Properly Paired	92.0800	94.1100
With itself	57217719	97482566
With itself(QC-failed)	0	0
Singletons	334578	816820
Singletons(QC-failed)	0	0
% Singleton	0.5500	0.8000
Diff. Chroms	471851	1199069
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	25507747	41555789
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	88498	219396
Paired Opt. Dupes	579	598
% Dupes/100	0.0035	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25506261	41491091
Distinct Read Pairs	25417767	41273018
One Read Pair	25329552	41056255
Two Read Pairs	87937	215467
NRF = Distinct/Total	0.9965	0.9947
PBC1 = OnePair/Distinct	0.9965	0.9947
PBC2 = OnePair/TwoPair	288.0420	190.5454

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	50838498	82672786
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50838498	82672786
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50838498	82672786
Paired(QC-failed)	0	0
Read1	25419249	41336393
Read1(QC-failed)	0	0
Read2	25419249	41336393
Read2(QC-failed)	0	0
Properly Paired	50838498	82672786
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50838498	82672786
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	137851
Np	0
N optimal	137851
N conservative	137851
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.	0.1868
Phantom Peak	50
Corr. Phantom Peak	0.1934
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0550
RSC	0.5962

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	0.1939

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	0.2106
AUC	0.4943
CHANCE divergence	0.1553
Elbow Point	0.0000
JS Distance	0.6741
Synthetic AUC	0.4964
Synthetic Elbow Point	0.1160
Synthetic JS Distance	0.3717