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Report generated at 2020-05-03 10:00:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	83273110	113987742
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70003825	105961159
Mapped(QC-failed)	0	0
% Mapped	84.0700	92.9600
Paired	83273110	113987742
Paired(QC-failed)	0	0
Read1	41636555	56993871
Read1(QC-failed)	0	0
Read2	41636555	56993871
Read2(QC-failed)	0	0
Properly Paired	62565389	90037210
Properly Paired(QC-failed)	0	0
% Properly Paired	75.1300	78.9900
With itself	66508574	102013829
With itself(QC-failed)	0	0
Singletons	3495251	3947330
Singletons(QC-failed)	0	0
% Singleton	4.2000	3.4600
Diff. Chroms	1790905	8799460
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	22866775	33432972
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	257139	558302
Paired Opt. Dupes	503	789
% Dupes/100	0.0112	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22866522	33432710
Distinct Read Pairs	22609383	32874411
One Read Pair	22355253	32324786
Two Read Pairs	251159	541092
NRF = Distinct/Total	0.9888	0.9833
PBC1 = OnePair/Distinct	0.9888	0.9833
PBC2 = OnePair/TwoPair	89.0084	59.7399

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	45219272	65749340
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45219272	65749340
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45219272	65749340
Paired(QC-failed)	0	0
Read1	22609636	32874670
Read1(QC-failed)	0	0
Read2	22609636	32874670
Read2(QC-failed)	0	0
Properly Paired	45219272	65749340
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45219272	65749340
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	213337
Np	0
N optimal	213337
N conservative	213337
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.	0.2712
Phantom Peak	50
Corr. Phantom Peak	0.3055
Argmin. Corr.	1500
Min. Corr.	0.2148
NSC	1.2627
RSC	0.6218

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	0.4192

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	0.0969
AUC	0.4939
CHANCE divergence	0.4930
Elbow Point	0.0000
JS Distance	0.7476
Synthetic AUC	0.5049
Synthetic Elbow Point	0.1394
Synthetic JS Distance	0.4702