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Report generated at 2020-07-23 15:11:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	179420290	208397864
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	178202793	205001727
Mapped(QC-failed)	0	0
% Mapped	99.3200	98.3700
Paired	179420290	208397864
Paired(QC-failed)	0	0
Read1	89710145	104198932
Read1(QC-failed)	0	0
Read2	89710145	104198932
Read2(QC-failed)	0	0
Properly Paired	176977963	199305736
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6400	95.6400
With itself	177298533	203636968
With itself(QC-failed)	0	0
Singletons	904260	1364759
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6500
Diff. Chroms	87755	299296
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	82917884	87961350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	913405	1539702
Paired Opt. Dupes	3226	2336
% Dupes/100	0.0110	0.0175

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82909710	87956751
Distinct Read Pairs	81996649	86417421
One Read Pair	81106621	84991112
Two Read Pairs	868455	1357061
NRF = Distinct/Total	0.9890	0.9825
PBC1 = OnePair/Distinct	0.9891	0.9835
PBC2 = OnePair/TwoPair	93.3919	62.6288

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	164008958	172843296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	164008958	172843296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	164008958	172843296
Paired(QC-failed)	0	0
Read1	82004479	86421648
Read1(QC-failed)	0	0
Read2	82004479	86421648
Read2(QC-failed)	0	0
Properly Paired	164008958	172843296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	164008958	172843296
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	213709
Np	0
N optimal	213709
N conservative	213709
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.	-10
Corr. Est. Fragment Len.	0.1834
Phantom Peak	55
Corr. Phantom Peak	0.1783
Argmin. Corr.	1500
Min. Corr.	0.1766
NSC	1.0382
RSC	4.0397

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	0.4945

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	0.1874
AUC	0.4968
CHANCE divergence	0.1398
Elbow Point	0.0000
JS Distance	0.6907
Synthetic AUC	0.4982
Synthetic Elbow Point	0.2769
Synthetic JS Distance	0.4301