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Report generated at 2020-05-31 10:43:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	223196434	189647610
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	222027910	186420329
Mapped(QC-failed)	0	0
% Mapped	99.4800	98.3000
Paired	223196434	189647610
Paired(QC-failed)	0	0
Read1	111598217	94823805
Read1(QC-failed)	0	0
Read2	111598217	94823805
Read2(QC-failed)	0	0
Properly Paired	217163976	181392671
Properly Paired(QC-failed)	0	0
% Properly Paired	97.3000	95.6500
With itself	221333806	185501724
With itself(QC-failed)	0	0
Singletons	694104	918605
Singletons(QC-failed)	0	0
% Singleton	0.3100	0.4800
Diff. Chroms	147222	192426
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	101238599	79855328
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1121331	864526
Paired Opt. Dupes	5017	3559
% Dupes/100	0.0111	0.0108

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	101236766	79850870
Distinct Read Pairs	100115465	78986507
One Read Pair	99015702	78170714
Two Read Pairs	1079093	793031
NRF = Distinct/Total	0.9889	0.9892
PBC1 = OnePair/Distinct	0.9890	0.9897
PBC2 = OnePair/TwoPair	91.7583	98.5721

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	200234536	157981604
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	200234536	157981604
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	200234536	157981604
Paired(QC-failed)	0	0
Read1	100117268	78990802
Read1(QC-failed)	0	0
Read2	100117268	78990802
Read2(QC-failed)	0	0
Properly Paired	200234536	157981604
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	200234536	157981604
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	254639
Np	0
N optimal	254639
N conservative	254639
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.	0.1751
Phantom Peak	55
Corr. Phantom Peak	0.1724
Argmin. Corr.	1500
Min. Corr.	0.1717
NSC	1.0197
RSC	4.9118

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	0.2356

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	0.2505
AUC	0.4971
CHANCE divergence	0.1167
Elbow Point	0.0000
JS Distance	0.5970
Synthetic AUC	0.4989
Synthetic Elbow Point	0.1725
Synthetic JS Distance	0.3316