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Report generated at 2020-05-31 02:44:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	167295876	145880064
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	163673496	143543481
Mapped(QC-failed)	0	0
% Mapped	97.8300	98.4000
Paired	167295876	145880064
Paired(QC-failed)	0	0
Read1	83647938	72940032
Read1(QC-failed)	0	0
Read2	83647938	72940032
Read2(QC-failed)	0	0
Properly Paired	158310308	137661116
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6300	94.3700
With itself	162295135	142561671
With itself(QC-failed)	0	0
Singletons	1378361	981810
Singletons(QC-failed)	0	0
% Singleton	0.8200	0.6700
Diff. Chroms	181128	166692
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	68946857	60849040
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8451352	702465
Paired Opt. Dupes	2557	2258
% Dupes/100	0.1226	0.0115

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68927476	60831717
Distinct Read Pairs	60479886	60130769
One Read Pair	52886005	59468322
Two Read Pairs	6837415	649167
NRF = Distinct/Total	0.8774	0.9885
PBC1 = OnePair/Distinct	0.8744	0.9890
PBC2 = OnePair/TwoPair	7.7348	91.6071

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	120991010	120293150
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120991010	120293150
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	120991010	120293150
Paired(QC-failed)	0	0
Read1	60495505	60146575
Read1(QC-failed)	0	0
Read2	60495505	60146575
Read2(QC-failed)	0	0
Properly Paired	120991010	120293150
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	120991010	120293150
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	252730
Np	0
N optimal	252730
N conservative	252730
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.	125
Corr. Est. Fragment Len.	0.1862
Phantom Peak	50
Corr. Phantom Peak	0.1929
Argmin. Corr.	1500
Min. Corr.	0.1752
NSC	1.0630
RSC	0.6228

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	0.3685

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	0.2196
AUC	0.4963
CHANCE divergence	0.0971
Elbow Point	0.0000
JS Distance	0.7268
Synthetic AUC	0.5056
Synthetic Elbow Point	0.2617
Synthetic JS Distance	0.3857