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Report generated at 2020-05-02 12:48:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	30779182	45100544
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	29284376	42784977
Mapped(QC-failed)	0	0
% Mapped	95.1400	94.8700
Paired	30779182	45100544
Paired(QC-failed)	0	0
Read1	15389591	22550272
Read1(QC-failed)	0	0
Read2	15389591	22550272
Read2(QC-failed)	0	0
Properly Paired	28350834	34886479
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1100	77.3500
With itself	28838846	41495730
With itself(QC-failed)	0	0
Singletons	445530	1289247
Singletons(QC-failed)	0	0
% Singleton	1.4500	2.8600
Diff. Chroms	371520	4523333
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	12808790	13208684
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	132993	154251
Paired Opt. Dupes	2717	1783
% Dupes/100	0.0104	0.0117

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	12808729	13208667
Distinct Read Pairs	12675736	13054416
One Read Pair	12543773	12901708
Two Read Pairs	130944	151186
NRF = Distinct/Total	0.9896	0.9883
PBC1 = OnePair/Distinct	0.9896	0.9883
PBC2 = OnePair/TwoPair	95.7949	85.3367

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	25351594	26108866
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25351594	26108866
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	25351594	26108866
Paired(QC-failed)	0	0
Read1	12675797	13054433
Read1(QC-failed)	0	0
Read2	12675797	13054433
Read2(QC-failed)	0	0
Properly Paired	25351594	26108866
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	25351594	26108866
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	101062
Np	0
N optimal	101062
N conservative	101062
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 (14M)

	rep1
Reads	14319332
Est. Fragment Len.	255
Corr. Est. Fragment Len.	0.2674
Phantom Peak	50
Corr. Phantom Peak	0.2396
Argmin. Corr.	1500
Min. Corr.	0.2080
NSC	1.2853
RSC	1.8795

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	0.5466

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	0.0592
AUC	0.4919
CHANCE divergence	0.6066
Elbow Point	0.0000
JS Distance	0.8315
Synthetic AUC	0.5133
Synthetic Elbow Point	0.2670
Synthetic JS Distance	0.5351