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Report generated at 2021-12-31 07:50:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	41788148	110823572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41310638	109263081
Mapped(QC-failed)	0	0
% Mapped	98.8600	98.5900
Paired	41788148	110823572
Paired(QC-failed)	0	0
Read1	20894074	55411786
Read1(QC-failed)	0	0
Read2	20894074	55411786
Read2(QC-failed)	0	0
Properly Paired	39393072	99432483
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2700	89.7200
With itself	41101394	108603175
With itself(QC-failed)	0	0
Singletons	209244	659906
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6000
Diff. Chroms	1391126	6017113
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	18101975	44416373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	376078	432626
Paired Opt. Dupes	1128	1846
% Dupes/100	0.0208	0.0097

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	18092928	44406721
Distinct Read Pairs	17717284	43974914
One Read Pair	17379527	43564699
Two Read Pairs	311676	402407
NRF = Distinct/Total	0.9792	0.9903
PBC1 = OnePair/Distinct	0.9809	0.9907
PBC2 = OnePair/TwoPair	55.7615	108.2603

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	35451794	87967494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35451794	87967494
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	35451794	87967494
Paired(QC-failed)	0	0
Read1	17725897	43983747
Read1(QC-failed)	0	0
Read2	17725897	43983747
Read2(QC-failed)	0	0
Properly Paired	35451794	87967494
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	35451794	87967494
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	92135
Np	0
N optimal	92135
N conservative	92135
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.	160
Corr. Est. Fragment Len.	0.2333
Phantom Peak	55
Corr. Phantom Peak	0.1926
Argmin. Corr.	1500
Min. Corr.	0.1634
NSC	1.4278
RSC	2.3917

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	0.5345

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	0.1188
AUC	0.4932
CHANCE divergence	0.2703
Elbow Point	0.0000
JS Distance	0.8177
Synthetic AUC	0.4999
Synthetic Elbow Point	0.4305
Synthetic JS Distance	0.5284