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Report generated at 2019-10-25 15:34:33

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94952806	164317158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91885220	162006082
Mapped(QC-failed)	0	0
% Mapped	96.7700	98.5900
Paired	94952806	164317158
Paired(QC-failed)	0	0
Read1	47476403	82158579
Read1(QC-failed)	0	0
Read2	47476403	82158579
Read2(QC-failed)	0	0
Properly Paired	90370077	158686405
Properly Paired(QC-failed)	0	0
% Properly Paired	95.1700	96.5700
With itself	91328935	161193128
With itself(QC-failed)	0	0
Singletons	556285	812954
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.4900
Diff. Chroms	623879	1201289
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	39212135	66502967
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1436203	1918147
Paired Opt. Dupes	14469	14289
% Dupes/100	0.0366	0.0288

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39211962	66493940
Distinct Read Pairs	37775763	64576078
One Read Pair	36382742	62704334
Two Read Pairs	1350983	1827454
NRF = Distinct/Total	0.9634	0.9712
PBC1 = OnePair/Distinct	0.9631	0.9710
PBC2 = OnePair/TwoPair	26.9306	34.3124

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	75551864	129169640
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75551864	129169640
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75551864	129169640
Paired(QC-failed)	0	0
Read1	37775932	64584820
Read1(QC-failed)	0	0
Read2	37775932	64584820
Read2(QC-failed)	0	0
Properly Paired	75551864	129169640
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75551864	129169640
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	123786
Np	0
N optimal	123786
N conservative	123786
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.	165
Corr. Est. Fragment Len.	0.2240
Phantom Peak	50
Corr. Phantom Peak	0.2244
Argmin. Corr.	1500
Min. Corr.	0.2152
NSC	1.0412
RSC	0.9601

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	0.7519

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	0.0789
AUC	0.4944
CHANCE divergence	0.3239
Elbow Point	0.0000
JS Distance	0.8433
Synthetic AUC	0.5026
Synthetic Elbow Point	0.5170
Synthetic JS Distance	0.6101