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Report generated at 2020-05-03 15:43:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131354044	118522358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129144473	116921431
Mapped(QC-failed)	0	0
% Mapped	98.3200	98.6500
Paired	131354044	118522358
Paired(QC-failed)	0	0
Read1	65677022	59261179
Read1(QC-failed)	0	0
Read2	65677022	59261179
Read2(QC-failed)	0	0
Properly Paired	127271835	111554301
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8900	94.1200
With itself	128398363	116290293
With itself(QC-failed)	0	0
Singletons	746110	631138
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.5300
Diff. Chroms	76597	155795
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	56267320	49637685
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2355464	399141
Paired Opt. Dupes	4902	4222
% Dupes/100	0.0419	0.0080

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56259011	49626135
Distinct Read Pairs	53904042	49227867
One Read Pair	51655961	48851116
Two Read Pairs	2164179	369226
NRF = Distinct/Total	0.9581	0.9920
PBC1 = OnePair/Distinct	0.9583	0.9923
PBC2 = OnePair/TwoPair	23.8686	132.3068

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	107823712	98477088
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107823712	98477088
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107823712	98477088
Paired(QC-failed)	0	0
Read1	53911856	49238544
Read1(QC-failed)	0	0
Read2	53911856	49238544
Read2(QC-failed)	0	0
Properly Paired	107823712	98477088
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107823712	98477088
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	144006
Np	0
N optimal	144006
N conservative	144006
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.	135
Corr. Est. Fragment Len.	0.1756
Phantom Peak	50
Corr. Phantom Peak	0.1834
Argmin. Corr.	1500
Min. Corr.	0.1696
NSC	1.0350
RSC	0.4329

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	0.1371

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	0.2873
AUC	0.4961
CHANCE divergence	0.0990
Elbow Point	0.0000
JS Distance	0.5815
Synthetic AUC	0.5056
Synthetic Elbow Point	0.1104
Synthetic JS Distance	0.2732