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Report generated at 2020-06-06 00:26:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92691174	90237136
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69727607	83832538
Mapped(QC-failed)	0	0
% Mapped	75.2300	92.9000
Paired	92691174	90237136
Paired(QC-failed)	0	0
Read1	46345587	45118568
Read1(QC-failed)	0	0
Read2	46345587	45118568
Read2(QC-failed)	0	0
Properly Paired	67714309	78392546
Properly Paired(QC-failed)	0	0
% Properly Paired	73.0500	86.8700
With itself	69074240	82897712
With itself(QC-failed)	0	0
Singletons	653367	934826
Singletons(QC-failed)	0	0
% Singleton	0.7000	1.0400
Diff. Chroms	146654	160808
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	30831464	35122089
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	18262885	1093718
Paired Opt. Dupes	8421	12203
% Dupes/100	0.5923	0.0311

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30830249	35109675
Distinct Read Pairs	12568121	34016360
One Read Pair	5789205	32967894
Two Read Pairs	2762850	1012328
NRF = Distinct/Total	0.4077	0.9689
PBC1 = OnePair/Distinct	0.4606	0.9692
PBC2 = OnePair/TwoPair	2.0954	32.5664

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	25137158	68056742
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25137158	68056742
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	25137158	68056742
Paired(QC-failed)	0	0
Read1	12568579	34028371
Read1(QC-failed)	0	0
Read2	12568579	34028371
Read2(QC-failed)	0	0
Properly Paired	25137158	68056742
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	25137158	68056742
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	201250
Np	0
N optimal	201250
N conservative	201250
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.	95
Corr. Est. Fragment Len.	0.1277
Phantom Peak	50
Corr. Phantom Peak	0.1170
Argmin. Corr.	1500
Min. Corr.	0.1055
NSC	1.2100
RSC	1.9270

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	0.4394

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	0.1117
AUC	0.4919
CHANCE divergence	0.4457
Elbow Point	0.0000
JS Distance	0.7913
Synthetic AUC	0.4990
Synthetic Elbow Point	0.2831
Synthetic JS Distance	0.4444