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Report generated at 2019-10-12 11:30:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	11984150	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	5758452	86768459
Mapped(QC-failed)	0	0
% Mapped	48.0500	97.7100
Paired	11984150	88801120
Paired(QC-failed)	0	0
Read1	5992075	44400560
Read1(QC-failed)	0	0
Read2	5992075	44400560
Read2(QC-failed)	0	0
Properly Paired	5639687	85806359
Properly Paired(QC-failed)	0	0
% Properly Paired	47.0600	96.6300
With itself	5709978	86430737
With itself(QC-failed)	0	0
Singletons	48474	337722
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.3800
Diff. Chroms	5468	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	2567625	37886939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	321639	723026
Paired Opt. Dupes	606	3740
% Dupes/100	0.1253	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	2567242	37657060
Distinct Read Pairs	2245646	36953214
One Read Pair	1964349	36265585
Two Read Pairs	246229	673617
NRF = Distinct/Total	0.8747	0.9813
PBC1 = OnePair/Distinct	0.8747	0.9814
PBC2 = OnePair/TwoPair	7.9777	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	4491972	74327826
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	4491972	74327826
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	4491972	74327826
Paired(QC-failed)	0	0
Read1	2245986	37163913
Read1(QC-failed)	0	0
Read2	2245986	37163913
Read2(QC-failed)	0	0
Properly Paired	4491972	74327826
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	4491972	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	86948
Np	0
N optimal	86948
N conservative	86948
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 (2M)

	rep1
Reads	2923785
Est. Fragment Len.	125
Corr. Est. Fragment Len.	0.0623
Phantom Peak	50
Corr. Phantom Peak	0.0603
Argmin. Corr.	1500
Min. Corr.	0.0409
NSC	1.5232
RSC	1.1023

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	0.3647

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	0.0682
AUC	0.4808
CHANCE divergence	0.7432
Elbow Point	0.0000
JS Distance	0.7746
Synthetic AUC	0.5344
Synthetic Elbow Point	0.2725
Synthetic JS Distance	0.3561