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Report generated at 2020-05-14 09:15:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	93323170	85104728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	86828188	81834549
Mapped(QC-failed)	0	0
% Mapped	93.0400	96.1600
Paired	93323170	85104728
Paired(QC-failed)	0	0
Read1	46661585	42552364
Read1(QC-failed)	0	0
Read2	46661585	42552364
Read2(QC-failed)	0	0
Properly Paired	83617181	77417456
Properly Paired(QC-failed)	0	0
% Properly Paired	89.6000	90.9700
With itself	85211619	79446512
With itself(QC-failed)	0	0
Singletons	1616569	2388037
Singletons(QC-failed)	0	0
% Singleton	1.7300	2.8100
Diff. Chroms	888439	1421679
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	34274998	32647563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	967250	620344
Paired Opt. Dupes	6979	1489
% Dupes/100	0.0282	0.0190

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34273199	32646807
Distinct Read Pairs	33305997	32026480
One Read Pair	32361491	31415922
Two Read Pairs	922413	600925
NRF = Distinct/Total	0.9718	0.9810
PBC1 = OnePair/Distinct	0.9716	0.9809
PBC2 = OnePair/TwoPair	35.0835	52.2793

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	66615496	64054438
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66615496	64054438
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66615496	64054438
Paired(QC-failed)	0	0
Read1	33307748	32027219
Read1(QC-failed)	0	0
Read2	33307748	32027219
Read2(QC-failed)	0	0
Properly Paired	66615496	64054438
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66615496	64054438
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	172599
Np	0
N optimal	172599
N conservative	172599
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.	250
Corr. Est. Fragment Len.	0.2337
Phantom Peak	50
Corr. Phantom Peak	0.2337
Argmin. Corr.	1500
Min. Corr.	0.1927
NSC	1.2128
RSC	1.0005

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	0.3923

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	0.1275
AUC	0.4950
CHANCE divergence	0.3744
Elbow Point	0.0000
JS Distance	0.7107
Synthetic AUC	0.5055
Synthetic Elbow Point	0.2033
Synthetic JS Distance	0.4530