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Report generated at 2019-10-25 04:12:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	51591442	108051026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48826422	106769052
Mapped(QC-failed)	0	0
% Mapped	94.6400	98.8100
Paired	51591442	108051026
Paired(QC-failed)	0	0
Read1	25795721	54025513
Read1(QC-failed)	0	0
Read2	25795721	54025513
Read2(QC-failed)	0	0
Properly Paired	48224906	102974844
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4700	95.3000
With itself	48528167	106137917
With itself(QC-failed)	0	0
Singletons	298255	631135
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.5800
Diff. Chroms	181276	2007136
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	21460050	42899753
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2296018	909722
Paired Opt. Dupes	3499	7276
% Dupes/100	0.1070	0.0212

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21454032	42859157
Distinct Read Pairs	19158679	41950736
One Read Pair	17067701	41057737
Two Read Pairs	1902461	878320
NRF = Distinct/Total	0.8930	0.9788
PBC1 = OnePair/Distinct	0.8909	0.9787
PBC2 = OnePair/TwoPair	8.9714	46.7458

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	38328064	83980062
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38328064	83980062
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38328064	83980062
Paired(QC-failed)	0	0
Read1	19164032	41990031
Read1(QC-failed)	0	0
Read2	19164032	41990031
Read2(QC-failed)	0	0
Properly Paired	38328064	83980062
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38328064	83980062
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	25234
Np	0
N optimal	25234
N conservative	25234
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.	210
Corr. Est. Fragment Len.	0.4545
Phantom Peak	55
Corr. Phantom Peak	0.4138
Argmin. Corr.	1500
Min. Corr.	0.1939
NSC	2.3445
RSC	1.1853

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	0.6480

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	0.0811
AUC	0.4920
CHANCE divergence	0.3061
Elbow Point	0.0000
JS Distance	0.9232
Synthetic AUC	0.5116
Synthetic Elbow Point	0.5723
Synthetic JS Distance	0.6468