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Report generated at 2021-03-18 11:49:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	48040238	121174246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47300284	117800756
Mapped(QC-failed)	0	0
% Mapped	98.4600	97.2200
Paired	48040238	121174246
Paired(QC-failed)	0	0
Read1	24020119	60587123
Read1(QC-failed)	0	0
Read2	24020119	60587123
Read2(QC-failed)	0	0
Properly Paired	43725029	102846930
Properly Paired(QC-failed)	0	0
% Properly Paired	91.0200	84.8800
With itself	47013529	116568407
With itself(QC-failed)	0	0
Singletons	286755	1232349
Singletons(QC-failed)	0	0
% Singleton	0.6000	1.0200
Diff. Chroms	2533925	9653332
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	20222490	45723686
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	504367	412201
Paired Opt. Dupes	1750	1762
% Dupes/100	0.0249	0.0090

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	20210742	45718069
Distinct Read Pairs	19707329	45306289
One Read Pair	19278826	44922876
Two Read Pairs	379821	373109
NRF = Distinct/Total	0.9751	0.9910
PBC1 = OnePair/Distinct	0.9783	0.9915
PBC2 = OnePair/TwoPair	50.7577	120.4015

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	39436246	90622970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39436246	90622970
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	39436246	90622970
Paired(QC-failed)	0	0
Read1	19718123	45311485
Read1(QC-failed)	0	0
Read2	19718123	45311485
Read2(QC-failed)	0	0
Properly Paired	39436246	90622970
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	39436246	90622970
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	97863
Np	0
N optimal	97863
N conservative	97863
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.	165
Corr. Est. Fragment Len.	0.2496
Phantom Peak	55
Corr. Phantom Peak	0.2048
Argmin. Corr.	1500
Min. Corr.	0.1606
NSC	1.5542
RSC	2.0148

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	0.5634

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	0.1090
AUC	0.4935
CHANCE divergence	0.2712
Elbow Point	0.0000
JS Distance	0.8410
Synthetic AUC	0.5050
Synthetic Elbow Point	0.4628
Synthetic JS Distance	0.5560