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Report generated at 2019-10-12 14:06:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56937732	52163906
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54911469	51011229
Mapped(QC-failed)	0	0
% Mapped	96.4400	97.7900
Paired	56937732	52163906
Paired(QC-failed)	0	0
Read1	28468866	26081953
Read1(QC-failed)	0	0
Read2	28468866	26081953
Read2(QC-failed)	0	0
Properly Paired	54062952	50327538
Properly Paired(QC-failed)	0	0
% Properly Paired	94.9500	96.4800
With itself	54234761	50605281
With itself(QC-failed)	0	0
Singletons	676708	405948
Singletons(QC-failed)	0	0
% Singleton	1.1900	0.7800
Diff. Chroms	56723	116158
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	22338156	21583364
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	602822	577632
Paired Opt. Dupes	2338	1867
% Dupes/100	0.0270	0.0268

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22337542	21564897
Distinct Read Pairs	21734741	20987844
One Read Pair	21145866	20426550
Two Read Pairs	575282	546417
NRF = Distinct/Total	0.9730	0.9732
PBC1 = OnePair/Distinct	0.9729	0.9733
PBC2 = OnePair/TwoPair	36.7574	37.3827

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	43470668	42011464
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43470668	42011464
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43470668	42011464
Paired(QC-failed)	0	0
Read1	21735334	21005732
Read1(QC-failed)	0	0
Read2	21735334	21005732
Read2(QC-failed)	0	0
Properly Paired	43470668	42011464
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43470668	42011464
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	163596
Np	0
N optimal	163596
N conservative	163596
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.	130
Corr. Est. Fragment Len.	0.1789
Phantom Peak	50
Corr. Phantom Peak	0.1845
Argmin. Corr.	1500
Min. Corr.	0.1756
NSC	1.0191
RSC	0.3758

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	0.2412

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	0.2102
AUC	0.4938
CHANCE divergence	0.1574
Elbow Point	0.0000
JS Distance	0.6990
Synthetic AUC	0.4982
Synthetic Elbow Point	0.1909
Synthetic JS Distance	0.3709