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Report generated at 2020-06-05 22:10:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	134765648	94272842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132979827	92659557
Mapped(QC-failed)	0	0
% Mapped	98.6700	98.2900
Paired	134765648	94272842
Paired(QC-failed)	0	0
Read1	67382824	47136421
Read1(QC-failed)	0	0
Read2	67382824	47136421
Read2(QC-failed)	0	0
Properly Paired	132172838	91574742
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0800	97.1400
With itself	132507313	92304558
With itself(QC-failed)	0	0
Singletons	472514	354999
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.3800
Diff. Chroms	91987	370286
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	60041923	40575988
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13551018	1257392
Paired Opt. Dupes	3824	3763
% Dupes/100	0.2257	0.0310

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60013310	40180957
Distinct Read Pairs	46469160	38989114
One Read Pair	36041175	37836528
Two Read Pairs	7991996	1116568
NRF = Distinct/Total	0.7743	0.9703
PBC1 = OnePair/Distinct	0.7756	0.9704
PBC2 = OnePair/TwoPair	4.5097	33.8865

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	92981810	78637192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92981810	78637192
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92981810	78637192
Paired(QC-failed)	0	0
Read1	46490905	39318596
Read1(QC-failed)	0	0
Read2	46490905	39318596
Read2(QC-failed)	0	0
Properly Paired	92981810	78637192
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92981810	78637192
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	163703
Np	0
N optimal	163703
N conservative	163703
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.	180
Corr. Est. Fragment Len.	0.1673
Phantom Peak	50
Corr. Phantom Peak	0.1730
Argmin. Corr.	1500
Min. Corr.	0.1619
NSC	1.0337
RSC	0.4896

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	0.1846

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	0.2738
AUC	0.4958
CHANCE divergence	0.1057
Elbow Point	0.0000
JS Distance	0.6409
Synthetic AUC	0.5046
Synthetic Elbow Point	0.1436
Synthetic JS Distance	0.2867