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Report generated at 2021-07-07 12:11:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	110152608	32633358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108869654	32017375
Mapped(QC-failed)	0	0
% Mapped	98.8400	98.1100
Paired	110152608	32633358
Paired(QC-failed)	0	0
Read1	55076304	16316679
Read1(QC-failed)	0	0
Read2	55076304	16316679
Read2(QC-failed)	0	0
Properly Paired	103004397	31194037
Properly Paired(QC-failed)	0	0
% Properly Paired	93.5100	95.5900
With itself	108203400	31710601
With itself(QC-failed)	0	0
Singletons	666254	306774
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.9400
Diff. Chroms	4105285	307689
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	48089064	13749916
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1538178	466098
Paired Opt. Dupes	2802	702
% Dupes/100	0.0320	0.0339

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48068076	13728708
Distinct Read Pairs	46532785	13265289
One Read Pair	45047273	12815823
Two Read Pairs	1438182	436590
NRF = Distinct/Total	0.9681	0.9662
PBC1 = OnePair/Distinct	0.9681	0.9661
PBC2 = OnePair/TwoPair	31.3224	29.3544

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	93101772	26567636
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93101772	26567636
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	93101772	26567636
Paired(QC-failed)	0	0
Read1	46550886	13283818
Read1(QC-failed)	0	0
Read2	46550886	13283818
Read2(QC-failed)	0	0
Properly Paired	93101772	26567636
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	93101772	26567636
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	149670
Np	0
N optimal	149670
N conservative	149670
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.	-5
Corr. Est. Fragment Len.	0.1944
Phantom Peak	55
Corr. Phantom Peak	0.1876
Argmin. Corr.	1500
Min. Corr.	0.1847
NSC	1.0522
RSC	3.3543

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	0.5361

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	0.1241
AUC	0.4958
CHANCE divergence	0.2343
Elbow Point	0.0000
JS Distance	0.7791
Synthetic AUC	0.5033
Synthetic Elbow Point	0.2601
Synthetic JS Distance	0.5220