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Report generated at 2021-02-10 10:45:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	173716306	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	169527033	143500908
Mapped(QC-failed)	0	0
% Mapped	97.5900	96.7800
Paired	173716306	148269018
Paired(QC-failed)	0	0
Read1	86858153	74134509
Read1(QC-failed)	0	0
Read2	86858153	74134509
Read2(QC-failed)	0	0
Properly Paired	166441743	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8100	94.5800
With itself	167760299	141622671
With itself(QC-failed)	0	0
Singletons	1766734	1878237
Singletons(QC-failed)	0	0
% Singleton	1.0200	1.2700
Diff. Chroms	551109	652729
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	72155656	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	364962	523701
Paired Opt. Dupes	18883	14446
% Dupes/100	0.0051	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	72138287	57674075
Distinct Read Pairs	71773500	57472830
One Read Pair	71410676	57272993
Two Read Pairs	360908	198503
NRF = Distinct/Total	0.9949	0.9965
PBC1 = OnePair/Distinct	0.9949	0.9965
PBC2 = OnePair/TwoPair	197.8639	288.5246

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	143581388	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	143581388	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	143581388	117133936
Paired(QC-failed)	0	0
Read1	71790694	58566968
Read1(QC-failed)	0	0
Read2	71790694	58566968
Read2(QC-failed)	0	0
Properly Paired	143581388	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	143581388	117133936
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	62286
Np	0
N optimal	62286
N conservative	62286
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.	0.1803
Phantom Peak	50
Corr. Phantom Peak	0.1948
Argmin. Corr.	1500
Min. Corr.	0.1745
NSC	1.0332
RSC	0.2851

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	0.0474

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	0.3287
AUC	0.4966
CHANCE divergence	0.0968
Elbow Point	0.0000
JS Distance	0.5190
Synthetic AUC	0.5062
Synthetic Elbow Point	0.1111
Synthetic JS Distance	0.2080