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Report generated at 2020-05-02 11:30:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63785908	52392786
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61095132	49028461
Mapped(QC-failed)	0	0
% Mapped	95.7800	93.5800
Paired	63785908	52392786
Paired(QC-failed)	0	0
Read1	31892954	26196393
Read1(QC-failed)	0	0
Read2	31892954	26196393
Read2(QC-failed)	0	0
Properly Paired	59149563	42386284
Properly Paired(QC-failed)	0	0
% Properly Paired	92.7300	80.9000
With itself	60081812	47560814
With itself(QC-failed)	0	0
Singletons	1013320	1467647
Singletons(QC-failed)	0	0
% Singleton	1.5900	2.8000
Diff. Chroms	659017	3739781
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	26387309	17509183
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	199443	332500
Paired Opt. Dupes	2151	1946
% Dupes/100	0.0076	0.0190

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26386858	17509057
Distinct Read Pairs	26187419	17176560
One Read Pair	25989288	16849216
Two Read Pairs	196826	322257
NRF = Distinct/Total	0.9924	0.9810
PBC1 = OnePair/Distinct	0.9924	0.9809
PBC2 = OnePair/TwoPair	132.0419	52.2850

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	52375732	34353366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52375732	34353366
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52375732	34353366
Paired(QC-failed)	0	0
Read1	26187866	17176683
Read1(QC-failed)	0	0
Read2	26187866	17176683
Read2(QC-failed)	0	0
Properly Paired	52375732	34353366
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52375732	34353366
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	114766
Np	0
N optimal	114766
N conservative	114766
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.	240
Corr. Est. Fragment Len.	0.2097
Phantom Peak	50
Corr. Phantom Peak	0.2085
Argmin. Corr.	1500
Min. Corr.	0.1886
NSC	1.1123
RSC	1.0633

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	0.3168

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	0.1454
AUC	0.4943
CHANCE divergence	0.3050
Elbow Point	0.0000
JS Distance	0.7111
Synthetic AUC	0.5062
Synthetic Elbow Point	0.1840
Synthetic JS Distance	0.4421