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Report generated at 2021-02-06 08:41:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	116265162	114808036
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112757359	112966653
Mapped(QC-failed)	0	0
% Mapped	96.9800	98.4000
Paired	116265162	114808036
Paired(QC-failed)	0	0
Read1	58132581	57404018
Read1(QC-failed)	0	0
Read2	58132581	57404018
Read2(QC-failed)	0	0
Properly Paired	110175430	111166608
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7600	96.8300
With itself	111663544	112278723
With itself(QC-failed)	0	0
Singletons	1093815	687930
Singletons(QC-failed)	0	0
% Singleton	0.9400	0.6000
Diff. Chroms	139835	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	42533311	48311888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	587969	307480
Paired Opt. Dupes	67811	76418
% Dupes/100	0.0138	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42509099	48289765
Distinct Read Pairs	41922596	47983591
One Read Pair	41402375	47690244
Two Read Pairs	499423	287957
NRF = Distinct/Total	0.9862	0.9937
PBC1 = OnePair/Distinct	0.9876	0.9939
PBC2 = OnePair/TwoPair	82.9004	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	83890684	96008816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	83890684	96008816
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	83890684	96008816
Paired(QC-failed)	0	0
Read1	41945342	48004408
Read1(QC-failed)	0	0
Read2	41945342	48004408
Read2(QC-failed)	0	0
Properly Paired	83890684	96008816
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	83890684	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	175455
Np	0
N optimal	175455
N conservative	175455
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.	0.1854
Phantom Peak	50
Corr. Phantom Peak	0.2067
Argmin. Corr.	1500
Min. Corr.	0.1755
NSC	1.0567
RSC	0.3189

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	0.1693

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	0.2655
AUC	0.4954
CHANCE divergence	0.1048
Elbow Point	0.0000
JS Distance	0.6266
Synthetic AUC	0.5071
Synthetic Elbow Point	0.1113
Synthetic JS Distance	0.3016