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Report generated at 2020-06-05 19:53:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	95582672	50431816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92707625	48831892
Mapped(QC-failed)	0	0
% Mapped	96.9900	96.8300
Paired	95582672	50431816
Paired(QC-failed)	0	0
Read1	47791336	25215908
Read1(QC-failed)	0	0
Read2	47791336	25215908
Read2(QC-failed)	0	0
Properly Paired	91331544	47916697
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5500	95.0100
With itself	91913032	48429061
With itself(QC-failed)	0	0
Singletons	794593	402831
Singletons(QC-failed)	0	0
% Singleton	0.8300	0.8000
Diff. Chroms	126710	115649
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	38404135	21176027
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	532629	1364540
Paired Opt. Dupes	11887	7918
% Dupes/100	0.0139	0.0644

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38401763	21155539
Distinct Read Pairs	37869163	19792555
One Read Pair	37346582	18512617
Two Read Pairs	513844	1202837
NRF = Distinct/Total	0.9861	0.9356
PBC1 = OnePair/Distinct	0.9862	0.9353
PBC2 = OnePair/TwoPair	72.6808	15.3908

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	75743012	39622974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75743012	39622974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75743012	39622974
Paired(QC-failed)	0	0
Read1	37871506	19811487
Read1(QC-failed)	0	0
Read2	37871506	19811487
Read2(QC-failed)	0	0
Properly Paired	75743012	39622974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75743012	39622974
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	94427
Np	0
N optimal	94427
N conservative	94427
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.	120
Corr. Est. Fragment Len.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.2142
Argmin. Corr.	1500
Min. Corr.	0.1779
NSC	1.0625
RSC	0.3064

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	0.1451

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	0.2683
AUC	0.4953
CHANCE divergence	0.1060
Elbow Point	0.0000
JS Distance	0.6236
Synthetic AUC	0.5079
Synthetic Elbow Point	0.1394
Synthetic JS Distance	0.3061