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Report generated at 2020-06-05 19:57:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	136068288	90571450
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134867576	89141379
Mapped(QC-failed)	0	0
% Mapped	99.1200	98.4200
Paired	136068288	90571450
Paired(QC-failed)	0	0
Read1	68034144	45285725
Read1(QC-failed)	0	0
Read2	68034144	45285725
Read2(QC-failed)	0	0
Properly Paired	134251659	88372922
Properly Paired(QC-failed)	0	0
% Properly Paired	98.6600	97.5700
With itself	134441387	88783534
With itself(QC-failed)	0	0
Singletons	426189	357845
Singletons(QC-failed)	0	0
% Singleton	0.3100	0.4000
Diff. Chroms	77224	165234
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	63700103	39016419
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16492821	627775
Paired Opt. Dupes	6831	3638
% Dupes/100	0.2589	0.0161

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63697752	38965533
Distinct Read Pairs	47205556	38339409
One Read Pair	35041000	37725321
Two Read Pairs	8898745	603278
NRF = Distinct/Total	0.7411	0.9839
PBC1 = OnePair/Distinct	0.7423	0.9840
PBC2 = OnePair/TwoPair	3.9377	62.5339

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	94414564	76777288
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94414564	76777288
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	94414564	76777288
Paired(QC-failed)	0	0
Read1	47207282	38388644
Read1(QC-failed)	0	0
Read2	47207282	38388644
Read2(QC-failed)	0	0
Properly Paired	94414564	76777288
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	94414564	76777288
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	142770
Np	0
N optimal	142770
N conservative	142770
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.	170
Corr. Est. Fragment Len.	0.2325
Phantom Peak	55
Corr. Phantom Peak	0.2203
Argmin. Corr.	1500
Min. Corr.	0.1889
NSC	1.2306
RSC	1.3854

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	0.6055

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	0.1074
AUC	0.4958
CHANCE divergence	0.2077
Elbow Point	0.0000
JS Distance	0.8208
Synthetic AUC	0.5003
Synthetic Elbow Point	0.4591
Synthetic JS Distance	0.5729