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Report generated at 2020-05-14 17:31:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63687344	113987742
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54645006	105961159
Mapped(QC-failed)	0	0
% Mapped	85.8000	92.9600
Paired	63687344	113987742
Paired(QC-failed)	0	0
Read1	31843672	56993871
Read1(QC-failed)	0	0
Read2	31843672	56993871
Read2(QC-failed)	0	0
Properly Paired	51584411	90037210
Properly Paired(QC-failed)	0	0
% Properly Paired	81.0000	78.9900
With itself	53115290	102013829
With itself(QC-failed)	0	0
Singletons	1529716	3947330
Singletons(QC-failed)	0	0
% Singleton	2.4000	3.4600
Diff. Chroms	1038443	8799460
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	21570644	33432972
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	196659	558302
Paired Opt. Dupes	421	789
% Dupes/100	0.0091	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21570459	33432710
Distinct Read Pairs	21373801	32874411
One Read Pair	21178835	32324786
Two Read Pairs	193291	541092
NRF = Distinct/Total	0.9909	0.9833
PBC1 = OnePair/Distinct	0.9909	0.9833
PBC2 = OnePair/TwoPair	109.5697	59.7399

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	42747970	65749340
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42747970	65749340
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42747970	65749340
Paired(QC-failed)	0	0
Read1	21373985	32874670
Read1(QC-failed)	0	0
Read2	21373985	32874670
Read2(QC-failed)	0	0
Properly Paired	42747970	65749340
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42747970	65749340
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	158688
Np	0
N optimal	158688
N conservative	158688
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.	0.2403
Phantom Peak	50
Corr. Phantom Peak	0.2401
Argmin. Corr.	1500
Min. Corr.	0.2010
NSC	1.1959
RSC	1.0056

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	0.3414

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	0.0885
AUC	0.4938
CHANCE divergence	0.5195
Elbow Point	0.0000
JS Distance	0.7646
Synthetic AUC	0.4988
Synthetic Elbow Point	0.1191
Synthetic JS Distance	0.4798