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Report generated at 2021-02-06 05:35:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	116313898	114808036
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115352433	112966653
Mapped(QC-failed)	0	0
% Mapped	99.1700	98.4000
Paired	116313898	114808036
Paired(QC-failed)	0	0
Read1	58156949	57404018
Read1(QC-failed)	0	0
Read2	58156949	57404018
Read2(QC-failed)	0	0
Properly Paired	113664791	111166608
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7200	96.8300
With itself	114867626	112278723
With itself(QC-failed)	0	0
Singletons	484807	687930
Singletons(QC-failed)	0	0
% Singleton	0.4200	0.6000
Diff. Chroms	68561	128846
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	52346345	48311888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	465675	307480
Paired Opt. Dupes	35476	76418
% Dupes/100	0.0089	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52337462	48289765
Distinct Read Pairs	51872042	47983591
One Read Pair	51412738	47690244
Two Read Pairs	453887	287957
NRF = Distinct/Total	0.9911	0.9937
PBC1 = OnePair/Distinct	0.9911	0.9939
PBC2 = OnePair/TwoPair	113.2721	165.6159

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	103761340	96008816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103761340	96008816
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103761340	96008816
Paired(QC-failed)	0	0
Read1	51880670	48004408
Read1(QC-failed)	0	0
Read2	51880670	48004408
Read2(QC-failed)	0	0
Properly Paired	103761340	96008816
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103761340	96008816
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	217559
Np	0
N optimal	217559
N conservative	217559
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.	0.1773
Phantom Peak	55
Corr. Phantom Peak	0.1757
Argmin. Corr.	1500
Min. Corr.	0.1689
NSC	1.0499
RSC	1.2394

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	0.2613

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	0.2485
AUC	0.4959
CHANCE divergence	0.1081
Elbow Point	0.0000
JS Distance	0.6809
Synthetic AUC	0.5073
Synthetic Elbow Point	0.1524
Synthetic JS Distance	0.3300