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Report generated at 2021-02-10 06:55:33

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	99019036	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88901075	187969057
Mapped(QC-failed)	0	0
% Mapped	89.7800	97.0900
Paired	99019036	193594802
Paired(QC-failed)	0	0
Read1	49509518	96797401
Read1(QC-failed)	0	0
Read2	49509518	96797401
Read2(QC-failed)	0	0
Properly Paired	87763823	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	88.6300	95.1900
With itself	88469258	185784698
With itself(QC-failed)	0	0
Singletons	431817	2184359
Singletons(QC-failed)	0	0
% Singleton	0.4400	1.1300
Diff. Chroms	328332	610670
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	39043991	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	684766	539110
Paired Opt. Dupes	8104	19807
% Dupes/100	0.0175	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39029615	77646644
Distinct Read Pairs	38345143	77172156
One Read Pair	37670580	76701136
Two Read Pairs	664793	467668
NRF = Distinct/Total	0.9825	0.9939
PBC1 = OnePair/Distinct	0.9824	0.9939
PBC2 = OnePair/TwoPair	56.6651	164.0077

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	76718450	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76718450	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76718450	155345422
Paired(QC-failed)	0	0
Read1	38359225	77672711
Read1(QC-failed)	0	0
Read2	38359225	77672711
Read2(QC-failed)	0	0
Properly Paired	76718450	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76718450	155345422
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	135967
Np	0
N optimal	135967
N conservative	135967
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.	135
Corr. Est. Fragment Len.	0.1840
Phantom Peak	50
Corr. Phantom Peak	0.1920
Argmin. Corr.	1500
Min. Corr.	0.1750
NSC	1.0512
RSC	0.5283

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	0.1953

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	0.2550
AUC	0.4953
CHANCE divergence	0.1097
Elbow Point	0.0000
JS Distance	0.6279
Synthetic AUC	0.4974
Synthetic Elbow Point	0.2042
Synthetic JS Distance	0.3227