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Report generated at 2021-10-21 12:26:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	80242164	271900510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78520457	268867859
Mapped(QC-failed)	0	0
% Mapped	97.8500	98.8800
Paired	80242164	271900510
Paired(QC-failed)	0	0
Read1	40121082	135950255
Read1(QC-failed)	0	0
Read2	40121082	135950255
Read2(QC-failed)	0	0
Properly Paired	76797276	243997757
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7100	89.7400
With itself	77478384	266848954
With itself(QC-failed)	0	0
Singletons	1042073	2018905
Singletons(QC-failed)	0	0
% Singleton	1.3000	0.7400
Diff. Chroms	296938	17720672
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	32973069	102422784
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3802559	6269067
Paired Opt. Dupes	5412	15041
% Dupes/100	0.1153	0.0612

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32967241	102104617
Distinct Read Pairs	29165286	95885343
One Read Pair	25748005	90031317
Two Read Pairs	3066810	5511626
NRF = Distinct/Total	0.8847	0.9391
PBC1 = OnePair/Distinct	0.8828	0.9389
PBC2 = OnePair/TwoPair	8.3957	16.3348

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	58341020	192307434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58341020	192307434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58341020	192307434
Paired(QC-failed)	0	0
Read1	29170510	96153717
Read1(QC-failed)	0	0
Read2	29170510	96153717
Read2(QC-failed)	0	0
Properly Paired	58341020	192307434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58341020	192307434
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	93376
Np	0
N optimal	93376
N conservative	93376
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.	180
Corr. Est. Fragment Len.	0.1935
Phantom Peak	50
Corr. Phantom Peak	0.1873
Argmin. Corr.	1500
Min. Corr.	0.1684
NSC	1.1488
RSC	1.3236

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	0.2677

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	0.2281
AUC	0.4935
CHANCE divergence	0.1306
Elbow Point	0.0000
JS Distance	0.6868
Synthetic AUC	0.5018
Synthetic Elbow Point	0.2848
Synthetic JS Distance	0.3663