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Report generated at 2019-10-12 15:34:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	62820440	67922260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53669280	66671927
Mapped(QC-failed)	0	0
% Mapped	85.4300	98.1600
Paired	62820440	67922260
Paired(QC-failed)	0	0
Read1	31410220	33961130
Read1(QC-failed)	0	0
Read2	31410220	33961130
Read2(QC-failed)	0	0
Properly Paired	52729114	65974824
Properly Paired(QC-failed)	0	0
% Properly Paired	83.9400	97.1300
With itself	52968840	66190040
With itself(QC-failed)	0	0
Singletons	700440	481887
Singletons(QC-failed)	0	0
% Singleton	1.1100	0.7100
Diff. Chroms	57649	48298
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	22904495	29193017
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	837720	5293541
Paired Opt. Dupes	1845	2779
% Dupes/100	0.0366	0.1813

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22903615	29163738
Distinct Read Pairs	22065922	23873848
One Read Pair	21255393	19716184
Two Read Pairs	784168	3278409
NRF = Distinct/Total	0.9634	0.8186
PBC1 = OnePair/Distinct	0.9633	0.8258
PBC2 = OnePair/TwoPair	27.1057	6.0139

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	44133550	47798952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44133550	47798952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44133550	47798952
Paired(QC-failed)	0	0
Read1	22066775	23899476
Read1(QC-failed)	0	0
Read2	22066775	23899476
Read2(QC-failed)	0	0
Properly Paired	44133550	47798952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44133550	47798952
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	64714
Np	0
N optimal	64714
N conservative	64714
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.	140
Corr. Est. Fragment Len.	0.1776
Phantom Peak	50
Corr. Phantom Peak	0.1910
Argmin. Corr.	1500
Min. Corr.	0.1700
NSC	1.0443
RSC	0.3590

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	0.0857

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	0.2847
AUC	0.4938
CHANCE divergence	0.1209
Elbow Point	0.0000
JS Distance	0.5723
Synthetic AUC	0.4968
Synthetic Elbow Point	0.0858
Synthetic JS Distance	0.2624