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Report generated at 2020-06-07 16:54:49

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	202163068	87587868
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	195851976	85042789
Mapped(QC-failed)	0	0
% Mapped	96.8800	97.0900
Paired	202163068	87587868
Paired(QC-failed)	0	0
Read1	101081534	43793934
Read1(QC-failed)	0	0
Read2	101081534	43793934
Read2(QC-failed)	0	0
Properly Paired	193494876	83193523
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7100	94.9800
With itself	194262184	83956804
With itself(QC-failed)	0	0
Singletons	1589792	1085985
Singletons(QC-failed)	0	0
% Singleton	0.7900	1.2400
Diff. Chroms	325060	333057
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	86498325	36699121
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6217705	221052
Paired Opt. Dupes	22032	15569
% Dupes/100	0.0719	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	86495537	36659035
Distinct Read Pairs	80278033	36438723
One Read Pair	74460353	36222772
Two Read Pairs	5445432	213165
NRF = Distinct/Total	0.9281	0.9940
PBC1 = OnePair/Distinct	0.9275	0.9941
PBC2 = OnePair/TwoPair	13.6739	169.9283

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	160561240	72956138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160561240	72956138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	160561240	72956138
Paired(QC-failed)	0	0
Read1	80280620	36478069
Read1(QC-failed)	0	0
Read2	80280620	36478069
Read2(QC-failed)	0	0
Properly Paired	160561240	72956138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	160561240	72956138
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	127046
Np	0
N optimal	127046
N conservative	127046
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.	0.1799
Phantom Peak	50
Corr. Phantom Peak	0.1891
Argmin. Corr.	1500
Min. Corr.	0.1740
NSC	1.0335
RSC	0.3866

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	0.1751

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	0.2879
AUC	0.4968
CHANCE divergence	0.0988
Elbow Point	0.0000
JS Distance	0.6621
Synthetic AUC	0.4972
Synthetic Elbow Point	0.1416
Synthetic JS Distance	0.2811