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Report generated at 2020-05-20 19:06:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81211532	163903192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53438386	160420879
Mapped(QC-failed)	0	0
% Mapped	65.8000	97.8800
Paired	81211532	163903192
Paired(QC-failed)	0	0
Read1	40605766	81951596
Read1(QC-failed)	0	0
Read2	40605766	81951596
Read2(QC-failed)	0	0
Properly Paired	52359680	158734975
Properly Paired(QC-failed)	0	0
% Properly Paired	64.4700	96.8500
With itself	52660933	159739476
With itself(QC-failed)	0	0
Singletons	777453	681403
Singletons(QC-failed)	0	0
% Singleton	0.9600	0.4200
Diff. Chroms	92138	350799
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	23012239	69550649
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	154775	430368
Paired Opt. Dupes	1113	2814
% Dupes/100	0.0067	0.0062

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23006183	69493062
Distinct Read Pairs	22851461	69063958
One Read Pair	22697619	68639549
Two Read Pairs	152973	420276
NRF = Distinct/Total	0.9933	0.9938
PBC1 = OnePair/Distinct	0.9933	0.9939
PBC2 = OnePair/TwoPair	148.3766	163.3202

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	45714928	138240562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45714928	138240562
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45714928	138240562
Paired(QC-failed)	0	0
Read1	22857464	69120281
Read1(QC-failed)	0	0
Read2	22857464	69120281
Read2(QC-failed)	0	0
Properly Paired	45714928	138240562
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45714928	138240562
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	37396
Np	0
N optimal	37396
N conservative	37396
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.	125
Corr. Est. Fragment Len.	0.1852
Phantom Peak	50
Corr. Phantom Peak	0.2246
Argmin. Corr.	1500
Min. Corr.	0.1649
NSC	1.1228
RSC	0.3395

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	0.1148

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	0.2380
AUC	0.4940
CHANCE divergence	0.1531
Elbow Point	0.0000
JS Distance	0.6167
Synthetic AUC	0.4965
Synthetic Elbow Point	0.1446
Synthetic JS Distance	0.3324