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Report generated at 2020-05-03 10:50:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52991620	141274676
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51119576	128854233
Mapped(QC-failed)	0	0
% Mapped	96.4700	91.2100
Paired	52991620	141274676
Paired(QC-failed)	0	0
Read1	26495810	70637338
Read1(QC-failed)	0	0
Read2	26495810	70637338
Read2(QC-failed)	0	0
Properly Paired	50150822	93362363
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6400	66.0900
With itself	50723033	122463704
With itself(QC-failed)	0	0
Singletons	396543	6390529
Singletons(QC-failed)	0	0
% Singleton	0.7500	4.5200
Diff. Chroms	309001	22420827
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	22220627	29753335
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	122484	298571
Paired Opt. Dupes	481	729
% Dupes/100	0.0055	0.0100

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22194174	29733908
Distinct Read Pairs	22071966	29435851
One Read Pair	21950367	29140676
Two Read Pairs	120992	292322
NRF = Distinct/Total	0.9945	0.9900
PBC1 = OnePair/Distinct	0.9945	0.9900
PBC2 = OnePair/TwoPair	181.4200	99.6869

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	44196286	58909528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44196286	58909528
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44196286	58909528
Paired(QC-failed)	0	0
Read1	22098143	29454764
Read1(QC-failed)	0	0
Read2	22098143	29454764
Read2(QC-failed)	0	0
Properly Paired	44196286	58909528
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44196286	58909528
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	24394
Np	0
N optimal	24394
N conservative	24394
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.	200
Corr. Est. Fragment Len.	0.2976
Phantom Peak	50
Corr. Phantom Peak	0.2876
Argmin. Corr.	1500
Min. Corr.	0.1759
NSC	1.6914
RSC	1.0898

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	0.3397

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	0.1762
AUC	0.4939
CHANCE divergence	0.1694
Elbow Point	0.0000
JS Distance	0.7486
Synthetic AUC	0.5049
Synthetic Elbow Point	0.3464
Synthetic JS Distance	0.4694