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Report generated at 2019-10-12 23:55:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	89890768	91343384
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87266303	89445668
Mapped(QC-failed)	0	0
% Mapped	97.0800	97.9200
Paired	89890768	91343384
Paired(QC-failed)	0	0
Read1	44945384	45671692
Read1(QC-failed)	0	0
Read2	44945384	45671692
Read2(QC-failed)	0	0
Properly Paired	85730247	87213882
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3700	95.4800
With itself	86688910	88898595
With itself(QC-failed)	0	0
Singletons	577393	547073
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.6000
Diff. Chroms	122980	153599
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	38094290	38418387
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4733892	536154
Paired Opt. Dupes	10096	12827
% Dupes/100	0.1243	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38093826	38404064
Distinct Read Pairs	33359986	37868153
One Read Pair	29222532	37343686
Two Read Pairs	3614910	515076
NRF = Distinct/Total	0.8757	0.9860
PBC1 = OnePair/Distinct	0.8760	0.9861
PBC2 = OnePair/TwoPair	8.0839	72.5013

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	66720796	75764466
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66720796	75764466
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66720796	75764466
Paired(QC-failed)	0	0
Read1	33360398	37882233
Read1(QC-failed)	0	0
Read2	33360398	37882233
Read2(QC-failed)	0	0
Properly Paired	66720796	75764466
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66720796	75764466
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	201378
Np	0
N optimal	201378
N conservative	201378
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.	120
Corr. Est. Fragment Len.	0.1827
Phantom Peak	50
Corr. Phantom Peak	0.1906
Argmin. Corr.	1500
Min. Corr.	0.1768
NSC	1.0331
RSC	0.4254

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	0.4493

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	0.1721
AUC	0.4950
CHANCE divergence	0.1530
Elbow Point	0.0000
JS Distance	0.7671
Synthetic AUC	0.5038
Synthetic Elbow Point	0.3058
Synthetic JS Distance	0.4484