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Report generated at 2020-06-06 04:32:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	124080086	122679248
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122242379	120175352
Mapped(QC-failed)	0	0
% Mapped	98.5200	97.9600
Paired	124080086	122679248
Paired(QC-failed)	0	0
Read1	62040043	61339624
Read1(QC-failed)	0	0
Read2	62040043	61339624
Read2(QC-failed)	0	0
Properly Paired	121178410	119101476
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6600	97.0800
With itself	121602996	119559427
With itself(QC-failed)	0	0
Singletons	639383	615925
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5000
Diff. Chroms	114677	97521
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	54245791	52721864
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2848737	1210103
Paired Opt. Dupes	12203	11987
% Dupes/100	0.0525	0.0230

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54243485	52619289
Distinct Read Pairs	51394863	51415463
One Read Pair	48688474	50253974
Two Read Pairs	2572830	1130657
NRF = Distinct/Total	0.9475	0.9771
PBC1 = OnePair/Distinct	0.9473	0.9774
PBC2 = OnePair/TwoPair	18.9241	44.4467

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	102794108	103023522
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102794108	103023522
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	102794108	103023522
Paired(QC-failed)	0	0
Read1	51397054	51511761
Read1(QC-failed)	0	0
Read2	51397054	51511761
Read2(QC-failed)	0	0
Properly Paired	102794108	103023522
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	102794108	103023522
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	128945
Np	0
N optimal	128945
N conservative	128945
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.	195
Corr. Est. Fragment Len.	0.1829
Phantom Peak	50
Corr. Phantom Peak	0.1904
Argmin. Corr.	1500
Min. Corr.	0.1746
NSC	1.0474
RSC	0.5240

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	0.2625

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	0.2379
AUC	0.4960
CHANCE divergence	0.1168
Elbow Point	0.0000
JS Distance	0.6851
Synthetic AUC	0.5002
Synthetic Elbow Point	0.1742
Synthetic JS Distance	0.3506