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Report generated at 2019-10-13 00:38:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108409628	103045968
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100366022	98644909
Mapped(QC-failed)	0	0
% Mapped	92.5800	95.7300
Paired	108409628	103045968
Paired(QC-failed)	0	0
Read1	54204814	51522984
Read1(QC-failed)	0	0
Read2	54204814	51522984
Read2(QC-failed)	0	0
Properly Paired	93406618	94442742
Properly Paired(QC-failed)	0	0
% Properly Paired	86.1600	91.6500
With itself	93978349	95330195
With itself(QC-failed)	0	0
Singletons	6387673	3314714
Singletons(QC-failed)	0	0
% Singleton	5.8900	3.2200
Diff. Chroms	363643	525356
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	40059344	40142171
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4642267	1418352
Paired Opt. Dupes	3502	4354
% Dupes/100	0.1159	0.0353

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40058717	40110587
Distinct Read Pairs	35416517	38693616
One Read Pair	31312392	37331634
Two Read Pairs	3628819	1311985
NRF = Distinct/Total	0.8841	0.9647
PBC1 = OnePair/Distinct	0.8841	0.9648
PBC2 = OnePair/TwoPair	8.6288	28.4543

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	70834154	77447638
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70834154	77447638
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70834154	77447638
Paired(QC-failed)	0	0
Read1	35417077	38723819
Read1(QC-failed)	0	0
Read2	35417077	38723819
Read2(QC-failed)	0	0
Properly Paired	70834154	77447638
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70834154	77447638
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	90835
Np	0
N optimal	90835
N conservative	90835
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.	145
Corr. Est. Fragment Len.	0.2392
Phantom Peak	50
Corr. Phantom Peak	0.2314
Argmin. Corr.	1500
Min. Corr.	0.1910
NSC	1.2522
RSC	1.1928

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	0.3994

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	0.1759
AUC	0.4951
CHANCE divergence	0.1325
Elbow Point	0.0000
JS Distance	0.7910
Synthetic AUC	0.5068
Synthetic Elbow Point	0.3541
Synthetic JS Distance	0.4688