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Report generated at 2020-05-20 20:01:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	172234606	116197260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	171031434	114125531
Mapped(QC-failed)	0	0
% Mapped	99.3000	98.2200
Paired	172234606	116197260
Paired(QC-failed)	0	0
Read1	86117303	58098630
Read1(QC-failed)	0	0
Read2	86117303	58098630
Read2(QC-failed)	0	0
Properly Paired	170244789	111936342
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8400	96.3300
With itself	170408709	113460777
With itself(QC-failed)	0	0
Singletons	622725	664754
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.5700
Diff. Chroms	39783	109989
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	79456153	49424273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2640180	404585
Paired Opt. Dupes	2609	1429
% Dupes/100	0.0332	0.0082

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	79454192	49418586
Distinct Read Pairs	76814087	49014360
One Read Pair	74295591	48629916
Two Read Pairs	2408602	376015
NRF = Distinct/Total	0.9668	0.9918
PBC1 = OnePair/Distinct	0.9672	0.9922
PBC2 = OnePair/TwoPair	30.8459	129.3297

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	153631946	98039376
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	153631946	98039376
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	153631946	98039376
Paired(QC-failed)	0	0
Read1	76815973	49019688
Read1(QC-failed)	0	0
Read2	76815973	49019688
Read2(QC-failed)	0	0
Properly Paired	153631946	98039376
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	153631946	98039376
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	277411
Np	0
N optimal	277411
N conservative	277411
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.	0.1921
Phantom Peak	55
Corr. Phantom Peak	0.1839
Argmin. Corr.	1500
Min. Corr.	0.1711
NSC	1.1226
RSC	1.6400

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	0.5365

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	0.1672
AUC	0.4967
CHANCE divergence	0.1129
Elbow Point	0.0000
JS Distance	0.7739
Synthetic AUC	0.4997
Synthetic Elbow Point	0.3308
Synthetic JS Distance	0.4771