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Report generated at 2019-10-12 17:24:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	66653966	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53866613	86768459
Mapped(QC-failed)	0	0
% Mapped	80.8200	97.7100
Paired	66653966	88801120
Paired(QC-failed)	0	0
Read1	33326983	44400560
Read1(QC-failed)	0	0
Read2	33326983	44400560
Read2(QC-failed)	0	0
Properly Paired	53070490	85806359
Properly Paired(QC-failed)	0	0
% Properly Paired	79.6200	96.6300
With itself	53586194	86430737
With itself(QC-failed)	0	0
Singletons	280419	337722
Singletons(QC-failed)	0	0
% Singleton	0.4200	0.3800
Diff. Chroms	40927	102712
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	24607206	37886939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5996619	723026
Paired Opt. Dupes	4179	3740
% Dupes/100	0.2437	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24605196	37657060
Distinct Read Pairs	18609073	36953214
One Read Pair	14027453	36265585
Two Read Pairs	3493833	673617
NRF = Distinct/Total	0.7563	0.9813
PBC1 = OnePair/Distinct	0.7538	0.9814
PBC2 = OnePair/TwoPair	4.0149	53.8371

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	37221174	74327826
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37221174	74327826
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	37221174	74327826
Paired(QC-failed)	0	0
Read1	18610587	37163913
Read1(QC-failed)	0	0
Read2	18610587	37163913
Read2(QC-failed)	0	0
Properly Paired	37221174	74327826
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	37221174	74327826
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	183788
Np	0
N optimal	183788
N conservative	183788
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.	0.1663
Phantom Peak	50
Corr. Phantom Peak	0.1648
Argmin. Corr.	1500
Min. Corr.	0.1539
NSC	1.0809
RSC	1.1393

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	0.3280

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	0.1746
AUC	0.4933
CHANCE divergence	0.2279
Elbow Point	0.0000
JS Distance	0.7141
Synthetic AUC	0.5104
Synthetic Elbow Point	0.2613
Synthetic JS Distance	0.4064