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Report generated at 2020-05-15 03:22:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108961444	144095950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106662886	133456854
Mapped(QC-failed)	0	0
% Mapped	97.8900	92.6200
Paired	108961444	144095950
Paired(QC-failed)	0	0
Read1	54480722	72047975
Read1(QC-failed)	0	0
Read2	54480722	72047975
Read2(QC-failed)	0	0
Properly Paired	104849121	100085786
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2300	69.4600
With itself	105995136	127614780
With itself(QC-failed)	0	0
Singletons	667750	5842074
Singletons(QC-failed)	0	0
% Singleton	0.6100	4.0500
Diff. Chroms	687628	21841128
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	45229093	33283608
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	743068	401960
Paired Opt. Dupes	1255	902
% Dupes/100	0.0164	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45182377	33264694
Distinct Read Pairs	44440424	32863263
One Read Pair	43709951	32466574
Two Read Pairs	719170	392011
NRF = Distinct/Total	0.9836	0.9879
PBC1 = OnePair/Distinct	0.9836	0.9879
PBC2 = OnePair/TwoPair	60.7783	82.8206

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	88972050	65763296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88972050	65763296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	88972050	65763296
Paired(QC-failed)	0	0
Read1	44486025	32881648
Read1(QC-failed)	0	0
Read2	44486025	32881648
Read2(QC-failed)	0	0
Properly Paired	88972050	65763296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	88972050	65763296
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	85239
Np	0
N optimal	85239
N conservative	85239
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.	150
Corr. Est. Fragment Len.	0.1879
Phantom Peak	50
Corr. Phantom Peak	0.2005
Argmin. Corr.	1500
Min. Corr.	0.1788
NSC	1.0508
RSC	0.4173

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	0.0766

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	0.2275
AUC	0.4957
CHANCE divergence	0.1567
Elbow Point	0.0000
JS Distance	0.6169
Synthetic AUC	0.4967
Synthetic Elbow Point	0.1156
Synthetic JS Distance	0.3490