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Report generated at 2020-07-14 11:51:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	37765200	46329162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30433899	42236467
Mapped(QC-failed)	0	0
% Mapped	80.5900	91.1700
Paired	37765200	46329162
Paired(QC-failed)	0	0
Read1	18882600	23164581
Read1(QC-failed)	0	0
Read2	18882600	23164581
Read2(QC-failed)	0	0
Properly Paired	28368667	32074327
Properly Paired(QC-failed)	0	0
% Properly Paired	75.1200	69.2300
With itself	29248291	40063456
With itself(QC-failed)	0	0
Singletons	1185608	2173011
Singletons(QC-failed)	0	0
% Singleton	3.1400	4.6900
Diff. Chroms	603010	5497695
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	12332972	11378098
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	225533	199719
Paired Opt. Dupes	1766	451
% Dupes/100	0.0183	0.0176

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	12332618	11378047
Distinct Read Pairs	12107090	11178330
One Read Pair	11884985	10981633
Two Read Pairs	218733	193730
NRF = Distinct/Total	0.9817	0.9824
PBC1 = OnePair/Distinct	0.9817	0.9824
PBC2 = OnePair/TwoPair	54.3356	56.6852

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	24214878	22356758
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24214878	22356758
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24214878	22356758
Paired(QC-failed)	0	0
Read1	12107439	11178379
Read1(QC-failed)	0	0
Read2	12107439	11178379
Read2(QC-failed)	0	0
Properly Paired	24214878	22356758
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24214878	22356758
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	49138
Np	0
N optimal	49138
N conservative	49138
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.	235
Corr. Est. Fragment Len.	0.2421
Phantom Peak	50
Corr. Phantom Peak	0.2278
Argmin. Corr.	1500
Min. Corr.	0.1823
NSC	1.3281
RSC	1.3142

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	0.2294

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	0.1179
AUC	0.4916
CHANCE divergence	0.4799
Elbow Point	0.0000
JS Distance	0.7007
Synthetic AUC	0.5141
Synthetic Elbow Point	0.1990
Synthetic JS Distance	0.4152