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Report generated at 2020-05-10 12:37:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	73088098	46329162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67996189	42236466
Mapped(QC-failed)	0	0
% Mapped	93.0300	91.1700
Paired	73088098	46329162
Paired(QC-failed)	0	0
Read1	36544049	23164581
Read1(QC-failed)	0	0
Read2	36544049	23164581
Read2(QC-failed)	0	0
Properly Paired	64504010	32074059
Properly Paired(QC-failed)	0	0
% Properly Paired	88.2600	69.2300
With itself	66526687	40063460
With itself(QC-failed)	0	0
Singletons	1469502	2173006
Singletons(QC-failed)	0	0
% Singleton	2.0100	4.6900
Diff. Chroms	1352542	5498059
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	27984447	11378400
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	185804	199707
Paired Opt. Dupes	4335	452
% Dupes/100	0.0066	0.0176

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27983255	11378350
Distinct Read Pairs	27797462	11178645
One Read Pair	27612706	10981955
Two Read Pairs	183723	193728
NRF = Distinct/Total	0.9934	0.9824
PBC1 = OnePair/Distinct	0.9934	0.9824
PBC2 = OnePair/TwoPair	150.2953	56.6875

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	55597286	22357386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55597286	22357386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55597286	22357386
Paired(QC-failed)	0	0
Read1	27798643	11178693
Read1(QC-failed)	0	0
Read2	27798643	11178693
Read2(QC-failed)	0	0
Properly Paired	55597286	22357386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55597286	22357386
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	90708
Np	0
N optimal	90708
N conservative	90708
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.	240
Corr. Est. Fragment Len.	0.2073
Phantom Peak	50
Corr. Phantom Peak	0.2041
Argmin. Corr.	1500
Min. Corr.	0.1865
NSC	1.1115
RSC	1.1785

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	0.2176

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	0.1425
AUC	0.4945
CHANCE divergence	0.3546
Elbow Point	0.0000
JS Distance	0.6851
Synthetic AUC	0.4952
Synthetic Elbow Point	0.1316
Synthetic JS Distance	0.4242