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Report generated at 2021-02-07 03:17:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	140616976	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	138364362	143500908
Mapped(QC-failed)	0	0
% Mapped	98.4000	96.7800
Paired	140616976	148269018
Paired(QC-failed)	0	0
Read1	70308488	74134509
Read1(QC-failed)	0	0
Read2	70308488	74134509
Read2(QC-failed)	0	0
Properly Paired	136227757	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8800	94.5800
With itself	137596941	141622671
With itself(QC-failed)	0	0
Singletons	767421	1878237
Singletons(QC-failed)	0	0
% Singleton	0.5500	1.2700
Diff. Chroms	789692	652729
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	60016417	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	403691	523701
Paired Opt. Dupes	11970	14446
% Dupes/100	0.0067	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60003700	57674075
Distinct Read Pairs	59600127	57472830
One Read Pair	59199266	57272993
Two Read Pairs	398176	198503
NRF = Distinct/Total	0.9933	0.9965
PBC1 = OnePair/Distinct	0.9933	0.9965
PBC2 = OnePair/TwoPair	148.6761	288.5246

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	119225452	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119225452	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	119225452	117133936
Paired(QC-failed)	0	0
Read1	59612726	58566968
Read1(QC-failed)	0	0
Read2	59612726	58566968
Read2(QC-failed)	0	0
Properly Paired	119225452	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	119225452	117133936
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	111959
Np	0
N optimal	111959
N conservative	111959
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.	155
Corr. Est. Fragment Len.	0.2082
Phantom Peak	50
Corr. Phantom Peak	0.2119
Argmin. Corr.	1500
Min. Corr.	0.1848
NSC	1.1266
RSC	0.8639

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	0.2804

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	0.2218
AUC	0.4963
CHANCE divergence	0.1175
Elbow Point	0.0000
JS Distance	0.6754
Synthetic AUC	0.5037
Synthetic Elbow Point	0.2835
Synthetic JS Distance	0.3903