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Report generated at 2019-10-13 04:34:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100440768	108591830
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96580887	106438037
Mapped(QC-failed)	0	0
% Mapped	96.1600	98.0200
Paired	100440768	108591830
Paired(QC-failed)	0	0
Read1	50220384	54295915
Read1(QC-failed)	0	0
Read2	50220384	54295915
Read2(QC-failed)	0	0
Properly Paired	94666210	105115729
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2500	96.8000
With itself	95461115	105717137
With itself(QC-failed)	0	0
Singletons	1119772	720900
Singletons(QC-failed)	0	0
% Singleton	1.1100	0.6600
Diff. Chroms	135464	99242
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	39122675	45922398
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3856338	1306085
Paired Opt. Dupes	5499	6911
% Dupes/100	0.0986	0.0284

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39118891	45880524
Distinct Read Pairs	35262868	44576417
One Read Pair	31785747	43329358
Two Read Pairs	3142534	1206791
NRF = Distinct/Total	0.9014	0.9716
PBC1 = OnePair/Distinct	0.9014	0.9720
PBC2 = OnePair/TwoPair	10.1147	35.9046

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	70532674	89232626
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70532674	89232626
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70532674	89232626
Paired(QC-failed)	0	0
Read1	35266337	44616313
Read1(QC-failed)	0	0
Read2	35266337	44616313
Read2(QC-failed)	0	0
Properly Paired	70532674	89232626
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70532674	89232626
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	56616
Np	0
N optimal	56616
N conservative	56616
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.	0.1927
Phantom Peak	50
Corr. Phantom Peak	0.2205
Argmin. Corr.	1500
Min. Corr.	0.1812
NSC	1.0639
RSC	0.2944

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	0.1247

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	0.2500
AUC	0.4951
CHANCE divergence	0.1307
Elbow Point	0.0000
JS Distance	0.6016
Synthetic AUC	0.4977
Synthetic Elbow Point	0.1184
Synthetic JS Distance	0.3243