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Report generated at 2020-06-05 16:08:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72756656	104471744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65992864	101485188
Mapped(QC-failed)	0	0
% Mapped	90.7000	97.1400
Paired	72756656	104471744
Paired(QC-failed)	0	0
Read1	36378328	52235872
Read1(QC-failed)	0	0
Read2	36378328	52235872
Read2(QC-failed)	0	0
Properly Paired	65032801	100570496
Properly Paired(QC-failed)	0	0
% Properly Paired	89.3800	96.2700
With itself	65492562	101112353
With itself(QC-failed)	0	0
Singletons	500302	372835
Singletons(QC-failed)	0	0
% Singleton	0.6900	0.3600
Diff. Chroms	102451	208160
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	26114701	44719965
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5444819	1561842
Paired Opt. Dupes	2229	6437
% Dupes/100	0.2085	0.0349

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26108933	44378069
Distinct Read Pairs	20665148	42863103
One Read Pair	16420113	41409228
Two Read Pairs	3318565	1404847
NRF = Distinct/Total	0.7915	0.9659
PBC1 = OnePair/Distinct	0.7946	0.9661
PBC2 = OnePair/TwoPair	4.9480	29.4760

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	41339764	86316246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41339764	86316246
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41339764	86316246
Paired(QC-failed)	0	0
Read1	20669882	43158123
Read1(QC-failed)	0	0
Read2	20669882	43158123
Read2(QC-failed)	0	0
Properly Paired	41339764	86316246
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41339764	86316246
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	83935
Np	0
N optimal	83935
N conservative	83935
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.	115
Corr. Est. Fragment Len.	0.1772
Phantom Peak	50
Corr. Phantom Peak	0.2088
Argmin. Corr.	1500
Min. Corr.	0.1644
NSC	1.0779
RSC	0.2882

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	0.0705

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	0.2476
AUC	0.4937
CHANCE divergence	0.1713
Elbow Point	0.0000
JS Distance	0.5990
Synthetic AUC	0.4986
Synthetic Elbow Point	0.1245
Synthetic JS Distance	0.2954