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Report generated at 2021-10-23 19:12:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	193627840	202350424
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	187767359	198649849
Mapped(QC-failed)	0	0
% Mapped	96.9700	98.1700
Paired	193627840	202350424
Paired(QC-failed)	0	0
Read1	96813920	101175212
Read1(QC-failed)	0	0
Read2	96813920	101175212
Read2(QC-failed)	0	0
Properly Paired	181682655	191032553
Properly Paired(QC-failed)	0	0
% Properly Paired	93.8300	94.4100
With itself	185311527	196787032
With itself(QC-failed)	0	0
Singletons	2455832	1862817
Singletons(QC-failed)	0	0
% Singleton	1.2700	0.9200
Diff. Chroms	1608045	4083046
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	66169751	79868417
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5204161	3252613
Paired Opt. Dupes	51463	36998
% Dupes/100	0.0786	0.0407

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	66168146	79802498
Distinct Read Pairs	60964100	76553268
One Read Pair	56111772	73415319
Two Read Pairs	4523420	3032014
NRF = Distinct/Total	0.9214	0.9593
PBC1 = OnePair/Distinct	0.9204	0.9590
PBC2 = OnePair/TwoPair	12.4047	24.2134

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	121931180	153231608
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121931180	153231608
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	121931180	153231608
Paired(QC-failed)	0	0
Read1	60965590	76615804
Read1(QC-failed)	0	0
Read2	60965590	76615804
Read2(QC-failed)	0	0
Properly Paired	121931180	153231608
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	121931180	153231608
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	181571
Np	0
N optimal	181571
N conservative	181571
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.	110
Corr. Est. Fragment Len.	0.1925
Phantom Peak	50
Corr. Phantom Peak	0.2245
Argmin. Corr.	1500
Min. Corr.	0.1852
NSC	1.0394
RSC	0.1860

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	0.1903

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	0.2393
AUC	0.4955
CHANCE divergence	0.1091
Elbow Point	0.0000
JS Distance	0.6120
Synthetic AUC	0.5083
Synthetic Elbow Point	0.2203
Synthetic JS Distance	0.3480