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Report generated at 2021-10-23 08:43:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	142273944	297361170
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129847065	291047932
Mapped(QC-failed)	0	0
% Mapped	91.2700	97.8800
Paired	142273944	297361170
Paired(QC-failed)	0	0
Read1	71136972	148680585
Read1(QC-failed)	0	0
Read2	71136972	148680585
Read2(QC-failed)	0	0
Properly Paired	125551071	280334875
Properly Paired(QC-failed)	0	0
% Properly Paired	88.2500	94.2700
With itself	126847121	288800610
With itself(QC-failed)	0	0
Singletons	2999944	2247322
Singletons(QC-failed)	0	0
% Singleton	2.1100	0.7600
Diff. Chroms	979928	6137618
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	57327218	117478324
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7623528	8499398
Paired Opt. Dupes	11727	27800
% Dupes/100	0.1330	0.0723

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57324903	117374697
Distinct Read Pairs	49701696	108884086
One Read Pair	42961943	100890040
Two Read Pairs	5949288	7526259
NRF = Distinct/Total	0.8670	0.9277
PBC1 = OnePair/Distinct	0.8644	0.9266
PBC2 = OnePair/TwoPair	7.2214	13.4051

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	99407380	217957852
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99407380	217957852
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	99407380	217957852
Paired(QC-failed)	0	0
Read1	49703690	108978926
Read1(QC-failed)	0	0
Read2	49703690	108978926
Read2(QC-failed)	0	0
Properly Paired	99407380	217957852
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	99407380	217957852
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	38873
Np	0
N optimal	38873
N conservative	38873
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.	245
Corr. Est. Fragment Len.	0.5687
Phantom Peak	55
Corr. Phantom Peak	0.4994
Argmin. Corr.	1500
Min. Corr.	0.2111
NSC	2.6940
RSC	1.2404

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	0.8874

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	0.0235
AUC	0.4950
CHANCE divergence	0.4067
Elbow Point	0.0000
JS Distance	0.9623
Synthetic AUC	0.5008
Synthetic Elbow Point	0.7867
Synthetic JS Distance	0.8163