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Report generated at 2021-03-18 21:56:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	125934966	140350086
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124225945	136223961
Mapped(QC-failed)	0	0
% Mapped	98.6400	97.0600
Paired	125934966	140350086
Paired(QC-failed)	0	0
Read1	62967483	70175043
Read1(QC-failed)	0	0
Read2	62967483	70175043
Read2(QC-failed)	0	0
Properly Paired	108991681	120532551
Properly Paired(QC-failed)	0	0
% Properly Paired	86.5500	85.8800
With itself	123289072	134681268
With itself(QC-failed)	0	0
Singletons	936873	1542693
Singletons(QC-failed)	0	0
% Singleton	0.7400	1.1000
Diff. Chroms	5956704	9773665
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	49412060	53789939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	648247	594512
Paired Opt. Dupes	2167	1824
% Dupes/100	0.0131	0.0111

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49404858	53785343
Distinct Read Pairs	48756931	53191094
One Read Pair	48130708	52633239
Two Read Pairs	610464	539980
NRF = Distinct/Total	0.9869	0.9890
PBC1 = OnePair/Distinct	0.9872	0.9895
PBC2 = OnePair/TwoPair	78.8428	97.4726

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	97527626	106390854
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97527626	106390854
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97527626	106390854
Paired(QC-failed)	0	0
Read1	48763813	53195427
Read1(QC-failed)	0	0
Read2	48763813	53195427
Read2(QC-failed)	0	0
Properly Paired	97527626	106390854
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97527626	106390854
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	187827
Np	0
N optimal	187827
N conservative	187827
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.	150
Corr. Est. Fragment Len.	0.1767
Phantom Peak	50
Corr. Phantom Peak	0.1750
Argmin. Corr.	1500
Min. Corr.	0.1708
NSC	1.0343
RSC	1.3830

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	0.1586

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	0.2557
AUC	0.4959
CHANCE divergence	0.1382
Elbow Point	0.0000
JS Distance	0.5770
Synthetic AUC	0.5066
Synthetic Elbow Point	0.1301
Synthetic JS Distance	0.3085