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Report generated at 2020-05-18 22:54:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96715378	188531594
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89123625	183497192
Mapped(QC-failed)	0	0
% Mapped	92.1500	97.3300
Paired	96715378	188531594
Paired(QC-failed)	0	0
Read1	48357689	94265797
Read1(QC-failed)	0	0
Read2	48357689	94265797
Read2(QC-failed)	0	0
Properly Paired	86664960	180692140
Properly Paired(QC-failed)	0	0
% Properly Paired	89.6100	95.8400
With itself	87882869	182539954
With itself(QC-failed)	0	0
Singletons	1240756	957238
Singletons(QC-failed)	0	0
% Singleton	1.2800	0.5100
Diff. Chroms	491468	942066
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	34222593	78941456
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	176686	448927
Paired Opt. Dupes	1901	2929
% Dupes/100	0.0052	0.0057

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34219074	78883545
Distinct Read Pairs	34042412	78435677
One Read Pair	33868958	77991934
Two Read Pairs	170604	439949
NRF = Distinct/Total	0.9948	0.9943
PBC1 = OnePair/Distinct	0.9949	0.9943
PBC2 = OnePair/TwoPair	198.5238	177.2749

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	68091814	156985058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68091814	156985058
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	68091814	156985058
Paired(QC-failed)	0	0
Read1	34045907	78492529
Read1(QC-failed)	0	0
Read2	34045907	78492529
Read2(QC-failed)	0	0
Properly Paired	68091814	156985058
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	68091814	156985058
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	153916
Np	0
N optimal	153916
N conservative	153916
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.	130
Corr. Est. Fragment Len.	0.1957
Phantom Peak	50
Corr. Phantom Peak	0.2366
Argmin. Corr.	1500
Min. Corr.	0.1837
NSC	1.0658
RSC	0.2285

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	0.1411

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	0.2567
AUC	0.4951
CHANCE divergence	0.1137
Elbow Point	0.0000
JS Distance	0.6180
Synthetic AUC	0.5021
Synthetic Elbow Point	0.1325
Synthetic JS Distance	0.3134