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Report generated at 2021-03-19 17:55:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	89820052	99621326
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87910442	94051400
Mapped(QC-failed)	0	0
% Mapped	97.8700	94.4100
Paired	89820052	99621326
Paired(QC-failed)	0	0
Read1	44910026	49810663
Read1(QC-failed)	0	0
Read2	44910026	49810663
Read2(QC-failed)	0	0
Properly Paired	82006124	80789855
Properly Paired(QC-failed)	0	0
% Properly Paired	91.3000	81.1000
With itself	87178076	92478072
With itself(QC-failed)	0	0
Singletons	732366	1573328
Singletons(QC-failed)	0	0
% Singleton	0.8200	1.5800
Diff. Chroms	3582473	6482076
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	37913743	36021470
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1536742	466934
Paired Opt. Dupes	1909	1238
% Dupes/100	0.0405	0.0130

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37850206	36005664
Distinct Read Pairs	36327854	35540777
One Read Pair	34860895	35090740
Two Read Pairs	1415217	442464
NRF = Distinct/Total	0.9598	0.9871
PBC1 = OnePair/Distinct	0.9596	0.9873
PBC2 = OnePair/TwoPair	24.6329	79.3076

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	72754002	71109072
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72754002	71109072
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72754002	71109072
Paired(QC-failed)	0	0
Read1	36377001	35554536
Read1(QC-failed)	0	0
Read2	36377001	35554536
Read2(QC-failed)	0	0
Properly Paired	72754002	71109072
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72754002	71109072
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	199139
Np	0
N optimal	199139
N conservative	199139
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.	0.1768
Phantom Peak	55
Corr. Phantom Peak	0.1749
Argmin. Corr.	1500
Min. Corr.	0.1718
NSC	1.0287
RSC	1.5861

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	0.3318

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	0.2154
AUC	0.4952
CHANCE divergence	0.1198
Elbow Point	0.0000
JS Distance	0.7111
Synthetic AUC	0.5013
Synthetic Elbow Point	0.2320
Synthetic JS Distance	0.3806