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Report generated at 2020-07-14 21:06:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	44060764	161541774
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40341351	157457809
Mapped(QC-failed)	0	0
% Mapped	91.5600	97.4700
Paired	44060764	161541774
Paired(QC-failed)	0	0
Read1	22030382	80770887
Read1(QC-failed)	0	0
Read2	22030382	80770887
Read2(QC-failed)	0	0
Properly Paired	39791031	154923170
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3100	95.9000
With itself	40050035	156706856
With itself(QC-failed)	0	0
Singletons	291316	750953
Singletons(QC-failed)	0	0
% Singleton	0.6600	0.4600
Diff. Chroms	107744	1033935
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	17373852	67677947
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	77479	255439
Paired Opt. Dupes	6998	1182
% Dupes/100	0.0045	0.0038

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	17371359	67623047
Distinct Read Pairs	17293895	67368479
One Read Pair	17216678	67115243
Two Read Pairs	76972	251987
NRF = Distinct/Total	0.9955	0.9962
PBC1 = OnePair/Distinct	0.9955	0.9962
PBC2 = OnePair/TwoPair	223.6746	266.3441

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	34592746	134845016
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34592746	134845016
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	34592746	134845016
Paired(QC-failed)	0	0
Read1	17296373	67422508
Read1(QC-failed)	0	0
Read2	17296373	67422508
Read2(QC-failed)	0	0
Properly Paired	34592746	134845016
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	34592746	134845016
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	39960
Np	0
N optimal	39960
N conservative	39960
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.	120
Corr. Est. Fragment Len.	0.1882
Phantom Peak	50
Corr. Phantom Peak	0.2115
Argmin. Corr.	1500
Min. Corr.	0.1723
NSC	1.0925
RSC	0.4056

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	0.1068

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	0.2657
AUC	0.4931
CHANCE divergence	0.1329
Elbow Point	0.0000
JS Distance	0.5903
Synthetic AUC	0.5129
Synthetic Elbow Point	0.1613
Synthetic JS Distance	0.2940