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Report generated at 2020-05-02 13:52:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	44547972	55171578
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38912044	47068627
Mapped(QC-failed)	0	0
% Mapped	87.3500	85.3100
Paired	44547972	55171578
Paired(QC-failed)	0	0
Read1	22273986	27585789
Read1(QC-failed)	0	0
Read2	22273986	27585789
Read2(QC-failed)	0	0
Properly Paired	36593151	35348053
Properly Paired(QC-failed)	0	0
% Properly Paired	82.1400	64.0700
With itself	37869181	44252810
With itself(QC-failed)	0	0
Singletons	1042863	2815817
Singletons(QC-failed)	0	0
% Singleton	2.3400	5.1000
Diff. Chroms	899314	5846948
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	15900931	12505350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	166005	404711
Paired Opt. Dupes	1535	2139
% Dupes/100	0.0104	0.0324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15896161	12502680
Distinct Read Pairs	15730222	12098062
One Read Pair	15565768	11705353
Two Read Pairs	162981	381354
NRF = Distinct/Total	0.9896	0.9676
PBC1 = OnePair/Distinct	0.9895	0.9675
PBC2 = OnePair/TwoPair	95.5066	30.6942

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	31469852	24201278
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	31469852	24201278
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	31469852	24201278
Paired(QC-failed)	0	0
Read1	15734926	12100639
Read1(QC-failed)	0	0
Read2	15734926	12100639
Read2(QC-failed)	0	0
Properly Paired	31469852	24201278
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	31469852	24201278
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	45450
Np	0
N optimal	45450
N conservative	45450
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.	230
Corr. Est. Fragment Len.	0.1885
Phantom Peak	50
Corr. Phantom Peak	0.1956
Argmin. Corr.	1500
Min. Corr.	0.1788
NSC	1.0542
RSC	0.5768

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	0.0634

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	0.1833
AUC	0.4927
CHANCE divergence	0.2761
Elbow Point	0.0000
JS Distance	0.6542
Synthetic AUC	0.4948
Synthetic Elbow Point	0.0866
Synthetic JS Distance	0.3613