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Report generated at 2019-10-31 18:49:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	127879952	258600350
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126539293	255308360
Mapped(QC-failed)	0	0
% Mapped	98.9500	98.7300
Paired	127879952	258600350
Paired(QC-failed)	0	0
Read1	63939976	129300175
Read1(QC-failed)	0	0
Read2	63939976	129300175
Read2(QC-failed)	0	0
Properly Paired	125149492	246805576
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8600	95.4400
With itself	126029232	253638863
With itself(QC-failed)	0	0
Singletons	510061	1669497
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.6500
Diff. Chroms	197997	3939809
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	51830727	102636351
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	21490529	13145537
Paired Opt. Dupes	14307	27145
% Dupes/100	0.4146	0.1281

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51830085	102579949
Distinct Read Pairs	30339814	89443009
One Read Pair	17528131	77822807
Two Read Pairs	7495084	10274703
NRF = Distinct/Total	0.5854	0.8719
PBC1 = OnePair/Distinct	0.5777	0.8701
PBC2 = OnePair/TwoPair	2.3386	7.5742

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	60680396	178981628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60680396	178981628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60680396	178981628
Paired(QC-failed)	0	0
Read1	30340198	89490814
Read1(QC-failed)	0	0
Read2	30340198	89490814
Read2(QC-failed)	0	0
Properly Paired	60680396	178981628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60680396	178981628
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	188352
Np	0
N optimal	188352
N conservative	188352
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.	195
Corr. Est. Fragment Len.	0.1440
Phantom Peak	50
Corr. Phantom Peak	0.1497
Argmin. Corr.	1500
Min. Corr.	0.1402
NSC	1.0274
RSC	0.4046

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	0.1721

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	0.2463
AUC	0.4936
CHANCE divergence	0.1422
Elbow Point	0.0000
JS Distance	0.6060
Synthetic AUC	0.5110
Synthetic Elbow Point	0.1883
Synthetic JS Distance	0.3111