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Report generated at 2019-11-03 11:49:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52882106	196869810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52094733	192216298
Mapped(QC-failed)	0	0
% Mapped	98.5100	97.6400
Paired	52882106	196869810
Paired(QC-failed)	0	0
Read1	26441053	98434905
Read1(QC-failed)	0	0
Read2	26441053	98434905
Read2(QC-failed)	0	0
Properly Paired	51593860	187412851
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5600	95.2000
With itself	51849399	190908042
With itself(QC-failed)	0	0
Singletons	245334	1308256
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.6600
Diff. Chroms	89884	1377453
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	23787139	83348574
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2092266	1654003
Paired Opt. Dupes	4374	15356
% Dupes/100	0.0880	0.0198

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23775760	83232910
Distinct Read Pairs	21684478	81583711
One Read Pair	19751445	79958418
Two Read Pairs	1785289	1602927
NRF = Distinct/Total	0.9120	0.9802
PBC1 = OnePair/Distinct	0.9109	0.9801
PBC2 = OnePair/TwoPair	11.0634	49.8828

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	43389746	163389142
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43389746	163389142
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43389746	163389142
Paired(QC-failed)	0	0
Read1	21694873	81694571
Read1(QC-failed)	0	0
Read2	21694873	81694571
Read2(QC-failed)	0	0
Properly Paired	43389746	163389142
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43389746	163389142
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	83023
Np	0
N optimal	83023
N conservative	83023
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.	200
Corr. Est. Fragment Len.	0.2014
Phantom Peak	50
Corr. Phantom Peak	0.1994
Argmin. Corr.	1500
Min. Corr.	0.1765
NSC	1.1413
RSC	1.0887

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	0.4187

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	0.1682
AUC	0.4938
CHANCE divergence	0.1761
Elbow Point	0.0000
JS Distance	0.7672
Synthetic AUC	0.4989
Synthetic Elbow Point	0.3827
Synthetic JS Distance	0.4589