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Report generated at 2020-06-06 00:04:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	101433402	185450298
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99823855	180391771
Mapped(QC-failed)	0	0
% Mapped	98.4100	97.2700
Paired	101433402	185450298
Paired(QC-failed)	0	0
Read1	50716701	92725149
Read1(QC-failed)	0	0
Read2	50716701	92725149
Read2(QC-failed)	0	0
Properly Paired	99005007	177507350
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6100	95.7200
With itself	99369300	178457309
With itself(QC-failed)	0	0
Singletons	454555	1934462
Singletons(QC-failed)	0	0
% Singleton	0.4500	1.0400
Diff. Chroms	125767	394701
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	43828939	78598989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3603635	59956294
Paired Opt. Dupes	7423	8736
% Dupes/100	0.0822	0.7628

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43827546	78541002
Distinct Read Pairs	40224032	18624795
One Read Pair	36884512	3838017
Two Read Pairs	3094727	3259688
NRF = Distinct/Total	0.9178	0.2371
PBC1 = OnePair/Distinct	0.9170	0.2061
PBC2 = OnePair/TwoPair	11.9185	1.1774

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	80450608	37285390
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80450608	37285390
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80450608	37285390
Paired(QC-failed)	0	0
Read1	40225304	18642695
Read1(QC-failed)	0	0
Read2	40225304	18642695
Read2(QC-failed)	0	0
Properly Paired	80450608	37285390
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80450608	37285390
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	7267
Np	0
N optimal	7267
N conservative	7267
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.	130
Corr. Est. Fragment Len.	0.1724
Phantom Peak	50
Corr. Phantom Peak	0.1822
Argmin. Corr.	1500
Min. Corr.	0.1685
NSC	1.0232
RSC	0.2852

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	0.0034

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	0.3218
AUC	0.4955
CHANCE divergence	0.1041
Elbow Point	0.0000
JS Distance	0.5131
Synthetic AUC	0.4989
Synthetic Elbow Point	0.0391
Synthetic JS Distance	0.2094