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Report generated at 2021-12-31 17:21:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103603342	73857574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101156567	71880916
Mapped(QC-failed)	0	0
% Mapped	97.6400	97.3200
Paired	103603342	73857574
Paired(QC-failed)	0	0
Read1	51801671	36928787
Read1(QC-failed)	0	0
Read2	51801671	36928787
Read2(QC-failed)	0	0
Properly Paired	91411694	56693280
Properly Paired(QC-failed)	0	0
% Properly Paired	88.2300	76.7600
With itself	100184721	70763351
With itself(QC-failed)	0	0
Singletons	971846	1117565
Singletons(QC-failed)	0	0
% Singleton	0.9400	1.5100
Diff. Chroms	4542338	11478644
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	40463287	24996827
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2303387	241052
Paired Opt. Dupes	1779	1015
% Dupes/100	0.0569	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40448428	24993555
Distinct Read Pairs	38146551	24752593
One Read Pair	35966354	24516128
Two Read Pairs	2072821	233547
NRF = Distinct/Total	0.9431	0.9904
PBC1 = OnePair/Distinct	0.9428	0.9904
PBC2 = OnePair/TwoPair	17.3514	104.9730

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	76319800	49511550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76319800	49511550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76319800	49511550
Paired(QC-failed)	0	0
Read1	38159900	24755775
Read1(QC-failed)	0	0
Read2	38159900	24755775
Read2(QC-failed)	0	0
Properly Paired	76319800	49511550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76319800	49511550
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	75519
Np	0
N optimal	75519
N conservative	75519
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.	0.1742
Phantom Peak	50
Corr. Phantom Peak	0.1774
Argmin. Corr.	1500
Min. Corr.	0.1672
NSC	1.0421
RSC	0.6899

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	0.0747

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	0.2903
AUC	0.4953
CHANCE divergence	0.1021
Elbow Point	0.0000
JS Distance	0.5797
Synthetic AUC	0.5035
Synthetic Elbow Point	0.0711
Synthetic JS Distance	0.2639