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Report generated at 2020-06-05 17:51:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104105326	104471744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101148935	101485188
Mapped(QC-failed)	0	0
% Mapped	97.1600	97.1400
Paired	104105326	104471744
Paired(QC-failed)	0	0
Read1	52052663	52235872
Read1(QC-failed)	0	0
Read2	52052663	52235872
Read2(QC-failed)	0	0
Properly Paired	99935766	100570496
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9900	96.2700
With itself	100755756	101112353
With itself(QC-failed)	0	0
Singletons	393179	372835
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.3600
Diff. Chroms	64805	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	45900870	44719965
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10612822	1561842
Paired Opt. Dupes	3324	6437
% Dupes/100	0.2312	0.0349

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45884870	44378069
Distinct Read Pairs	35276323	42863103
One Read Pair	26807024	41409228
Two Read Pairs	6723323	1404847
NRF = Distinct/Total	0.7688	0.9659
PBC1 = OnePair/Distinct	0.7599	0.9661
PBC2 = OnePair/TwoPair	3.9872	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	70576096	86316246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70576096	86316246
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70576096	86316246
Paired(QC-failed)	0	0
Read1	35288048	43158123
Read1(QC-failed)	0	0
Read2	35288048	43158123
Read2(QC-failed)	0	0
Properly Paired	70576096	86316246
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70576096	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	71913
Np	0
N optimal	71913
N conservative	71913
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.	145
Corr. Est. Fragment Len.	0.3135
Phantom Peak	55
Corr. Phantom Peak	0.2842
Argmin. Corr.	1500
Min. Corr.	0.1750
NSC	1.7911
RSC	1.2680

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	0.4761

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	0.1571
AUC	0.4951
CHANCE divergence	0.1311
Elbow Point	0.0000
JS Distance	0.8515
Synthetic AUC	0.5061
Synthetic Elbow Point	0.4384
Synthetic JS Distance	0.5240