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Report generated at 2020-06-05 23:50:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129870628	65898052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124266718	64625224
Mapped(QC-failed)	0	0
% Mapped	95.6900	98.0700
Paired	129870628	65898052
Paired(QC-failed)	0	0
Read1	64935314	32949026
Read1(QC-failed)	0	0
Read2	64935314	32949026
Read2(QC-failed)	0	0
Properly Paired	122639046	63833486
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4300	96.8700
With itself	123184750	64118603
With itself(QC-failed)	0	0
Singletons	1081968	506621
Singletons(QC-failed)	0	0
% Singleton	0.8300	0.7700
Diff. Chroms	113640	74019
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	52436423	28025050
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3421567	294266
Paired Opt. Dupes	4002	2128
% Dupes/100	0.0653	0.0105

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52431578	27554999
Distinct Read Pairs	49010321	27340362
One Read Pair	45772464	27129504
Two Read Pairs	3062921	207820
NRF = Distinct/Total	0.9347	0.9922
PBC1 = OnePair/Distinct	0.9339	0.9923
PBC2 = OnePair/TwoPair	14.9441	130.5433

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	98029712	55461568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98029712	55461568
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98029712	55461568
Paired(QC-failed)	0	0
Read1	49014856	27730784
Read1(QC-failed)	0	0
Read2	49014856	27730784
Read2(QC-failed)	0	0
Properly Paired	98029712	55461568
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98029712	55461568
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	71871
Np	0
N optimal	71871
N conservative	71871
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.	205
Corr. Est. Fragment Len.	0.1749
Phantom Peak	50
Corr. Phantom Peak	0.1837
Argmin. Corr.	1500
Min. Corr.	0.1709
NSC	1.0233
RSC	0.3127

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	0.0373

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	0.3058
AUC	0.4959
CHANCE divergence	0.1013
Elbow Point	0.0000
JS Distance	0.5275
Synthetic AUC	0.5070
Synthetic Elbow Point	0.0862
Synthetic JS Distance	0.2410