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Report generated at 2020-06-05 23:50:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100096432	185450298
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98038266	180391771
Mapped(QC-failed)	0	0
% Mapped	97.9400	97.2700
Paired	100096432	185450298
Paired(QC-failed)	0	0
Read1	50048216	92725149
Read1(QC-failed)	0	0
Read2	50048216	92725149
Read2(QC-failed)	0	0
Properly Paired	97156123	177507350
Properly Paired(QC-failed)	0	0
% Properly Paired	97.0600	95.7200
With itself	97528994	178457309
With itself(QC-failed)	0	0
Singletons	509272	1934462
Singletons(QC-failed)	0	0
% Singleton	0.5100	1.0400
Diff. Chroms	120295	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	43068677	78598989
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8978845	59956294
Paired Opt. Dupes	7372	8736
% Dupes/100	0.2085	0.7628

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43067702	78541002
Distinct Read Pairs	34089058	18624795
One Read Pair	26836383	3838017
Two Read Pairs	5837742	3259688
NRF = Distinct/Total	0.7915	0.2371
PBC1 = OnePair/Distinct	0.7872	0.2061
PBC2 = OnePair/TwoPair	4.5970	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	68179664	37285390
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68179664	37285390
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	68179664	37285390
Paired(QC-failed)	0	0
Read1	34089832	18642695
Read1(QC-failed)	0	0
Read2	34089832	18642695
Read2(QC-failed)	0	0
Properly Paired	68179664	37285390
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	68179664	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	46289
Np	0
N optimal	46289
N conservative	46289
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.	135
Corr. Est. Fragment Len.	0.1662
Phantom Peak	50
Corr. Phantom Peak	0.1779
Argmin. Corr.	1500
Min. Corr.	0.1606
NSC	1.0345
RSC	0.3206

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	0.0294

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	0.3061
AUC	0.4951
CHANCE divergence	0.1070
Elbow Point	0.0000
JS Distance	0.5487
Synthetic AUC	0.5058
Synthetic Elbow Point	0.0429
Synthetic JS Distance	0.2322