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Report generated at 2020-05-14 13:10:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	53795856	113987742
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51015322	105961159
Mapped(QC-failed)	0	0
% Mapped	94.8300	92.9600
Paired	53795856	113987742
Paired(QC-failed)	0	0
Read1	26897928	56993871
Read1(QC-failed)	0	0
Read2	26897928	56993871
Read2(QC-failed)	0	0
Properly Paired	50550563	90037210
Properly Paired(QC-failed)	0	0
% Properly Paired	93.9700	78.9900
With itself	50704375	102013829
With itself(QC-failed)	0	0
Singletons	310947	3947330
Singletons(QC-failed)	0	0
% Singleton	0.5800	3.4600
Diff. Chroms	96983	8799460
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	23274663	33432972
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	448523	558302
Paired Opt. Dupes	365	789
% Dupes/100	0.0193	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23274220	33432710
Distinct Read Pairs	22825700	32874411
One Read Pair	22385337	32324786
Two Read Pairs	432333	541092
NRF = Distinct/Total	0.9807	0.9833
PBC1 = OnePair/Distinct	0.9807	0.9833
PBC2 = OnePair/TwoPair	51.7780	59.7399

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	45652280	65749340
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45652280	65749340
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45652280	65749340
Paired(QC-failed)	0	0
Read1	22826140	32874670
Read1(QC-failed)	0	0
Read2	22826140	32874670
Read2(QC-failed)	0	0
Properly Paired	45652280	65749340
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45652280	65749340
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	31915
Np	0
N optimal	31915
N conservative	31915
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.	200
Corr. Est. Fragment Len.	0.5214
Phantom Peak	55
Corr. Phantom Peak	0.4420
Argmin. Corr.	1500
Min. Corr.	0.1672
NSC	3.1191
RSC	1.2888

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	0.6667

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	0.0421
AUC	0.4940
CHANCE divergence	0.5601
Elbow Point	0.0000
JS Distance	0.8765
Synthetic AUC	0.4950
Synthetic Elbow Point	0.4804
Synthetic JS Distance	0.6724