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Report generated at 2019-10-30 15:57:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102895760	140993220
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97202139	139041098
Mapped(QC-failed)	0	0
% Mapped	94.4700	98.6200
Paired	102895760	140993220
Paired(QC-failed)	0	0
Read1	51447880	70496610
Read1(QC-failed)	0	0
Read2	51447880	70496610
Read2(QC-failed)	0	0
Properly Paired	94053289	134740908
Properly Paired(QC-failed)	0	0
% Properly Paired	91.4100	95.5700
With itself	96244400	138315977
With itself(QC-failed)	0	0
Singletons	957739	725121
Singletons(QC-failed)	0	0
% Singleton	0.9300	0.5100
Diff. Chroms	1416142	2179951
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	39496052	56499814
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1453933	1540164
Paired Opt. Dupes	16813	14091
% Dupes/100	0.0368	0.0273

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39495588	56486240
Distinct Read Pairs	38041676	54946507
One Read Pair	36632120	53441534
Two Read Pairs	1366476	1471338
NRF = Distinct/Total	0.9632	0.9727
PBC1 = OnePair/Distinct	0.9629	0.9726
PBC2 = OnePair/TwoPair	26.8077	36.3217

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	76084238	109919300
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76084238	109919300
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76084238	109919300
Paired(QC-failed)	0	0
Read1	38042119	54959650
Read1(QC-failed)	0	0
Read2	38042119	54959650
Read2(QC-failed)	0	0
Properly Paired	76084238	109919300
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76084238	109919300
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	142253
Np	0
N optimal	142253
N conservative	142253
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.	120
Corr. Est. Fragment Len.	0.1846
Phantom Peak	50
Corr. Phantom Peak	0.1922
Argmin. Corr.	1500
Min. Corr.	0.1799
NSC	1.0261
RSC	0.3809

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	0.1696

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	0.2427
AUC	0.4945
CHANCE divergence	0.1319
Elbow Point	0.0000
JS Distance	0.6188
Synthetic AUC	0.5047
Synthetic Elbow Point	0.1886
Synthetic JS Distance	0.3291