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Report generated at 2019-10-25 13:59:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	119997998	127273172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118125270	125877623
Mapped(QC-failed)	0	0
% Mapped	98.4400	98.9000
Paired	119997998	127273172
Paired(QC-failed)	0	0
Read1	59998999	63636586
Read1(QC-failed)	0	0
Read2	59998999	63636586
Read2(QC-failed)	0	0
Properly Paired	115381566	121731620
Properly Paired(QC-failed)	0	0
% Properly Paired	96.1500	95.6500
With itself	117403613	125137848
With itself(QC-failed)	0	0
Singletons	721657	739775
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.5800
Diff. Chroms	1438153	1957878
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	49824059	50825445
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4061322	3188108
Paired Opt. Dupes	8953	6482
% Dupes/100	0.0815	0.0627

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49823137	50816662
Distinct Read Pairs	45761876	47629109
One Read Pair	41950240	44580671
Two Read Pairs	3577033	2916506
NRF = Distinct/Total	0.9185	0.9373
PBC1 = OnePair/Distinct	0.9167	0.9360
PBC2 = OnePair/TwoPair	11.7277	15.2856

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	91525474	95274674
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91525474	95274674
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91525474	95274674
Paired(QC-failed)	0	0
Read1	45762737	47637337
Read1(QC-failed)	0	0
Read2	45762737	47637337
Read2(QC-failed)	0	0
Properly Paired	91525474	95274674
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91525474	95274674
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	61029
Np	0
N optimal	61029
N conservative	61029
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.	155
Corr. Est. Fragment Len.	0.2235
Phantom Peak	50
Corr. Phantom Peak	0.2229
Argmin. Corr.	1500
Min. Corr.	0.1834
NSC	1.2189
RSC	1.0147

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	0.3567

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	0.2155
AUC	0.4948
CHANCE divergence	0.1114
Elbow Point	0.0000
JS Distance	0.7843
Synthetic AUC	0.4995
Synthetic Elbow Point	0.3376
Synthetic JS Distance	0.4220