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Report generated at 2020-05-13 07:10:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	61023018	57562006
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56680316	55523694
Mapped(QC-failed)	0	0
% Mapped	92.8800	96.4600
Paired	61023018	57562006
Paired(QC-failed)	0	0
Read1	30511509	28781003
Read1(QC-failed)	0	0
Read2	30511509	28781003
Read2(QC-failed)	0	0
Properly Paired	54762427	51717909
Properly Paired(QC-failed)	0	0
% Properly Paired	89.7400	89.8500
With itself	55650020	54506329
With itself(QC-failed)	0	0
Singletons	1030296	1017365
Singletons(QC-failed)	0	0
% Singleton	1.6900	1.7700
Diff. Chroms	574311	1879530
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	24617081	22692587
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	271520	223060
Paired Opt. Dupes	2334	2088
% Dupes/100	0.0110	0.0098

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24616540	22686649
Distinct Read Pairs	24345026	22463666
One Read Pair	24076000	22242527
Two Read Pairs	266561	219310
NRF = Distinct/Total	0.9890	0.9902
PBC1 = OnePair/Distinct	0.9889	0.9902
PBC2 = OnePair/TwoPair	90.3208	101.4205

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	48691122	44939054
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48691122	44939054
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48691122	44939054
Paired(QC-failed)	0	0
Read1	24345561	22469527
Read1(QC-failed)	0	0
Read2	24345561	22469527
Read2(QC-failed)	0	0
Properly Paired	48691122	44939054
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48691122	44939054
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	71727
Np	0
N optimal	71727
N conservative	71727
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.	280
Corr. Est. Fragment Len.	0.2138
Phantom Peak	50
Corr. Phantom Peak	0.2063
Argmin. Corr.	1500
Min. Corr.	0.1840
NSC	1.1615
RSC	1.3343

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	0.3230

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	0.1456
AUC	0.4941
CHANCE divergence	0.3246
Elbow Point	0.0000
JS Distance	0.6972
Synthetic AUC	0.5097
Synthetic Elbow Point	0.2252
Synthetic JS Distance	0.4342