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Report generated at 2020-05-14 06:04:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72185162	74438840
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68704821	70461728
Mapped(QC-failed)	0	0
% Mapped	95.1800	94.6600
Paired	72185162	74438840
Paired(QC-failed)	0	0
Read1	36092581	37219420
Read1(QC-failed)	0	0
Read2	36092581	37219420
Read2(QC-failed)	0	0
Properly Paired	66970900	63045742
Properly Paired(QC-failed)	0	0
% Properly Paired	92.7800	84.6900
With itself	67654186	67777268
With itself(QC-failed)	0	0
Singletons	1050635	2684460
Singletons(QC-failed)	0	0
% Singleton	1.4600	3.6100
Diff. Chroms	414117	2894050
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	28551573	25565862
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	278839	413905
Paired Opt. Dupes	1496	1303
% Dupes/100	0.0098	0.0162

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28551172	25565508
Distinct Read Pairs	28272337	25151609
One Read Pair	27995829	24743478
Two Read Pairs	274203	402445
NRF = Distinct/Total	0.9902	0.9838
PBC1 = OnePair/Distinct	0.9902	0.9838
PBC2 = OnePair/TwoPair	102.0989	61.4829

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	56545468	50303914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	56545468	50303914
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	56545468	50303914
Paired(QC-failed)	0	0
Read1	28272734	25151957
Read1(QC-failed)	0	0
Read2	28272734	25151957
Read2(QC-failed)	0	0
Properly Paired	56545468	50303914
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	56545468	50303914
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	150143
Np	0
N optimal	150143
N conservative	150143
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.	250
Corr. Est. Fragment Len.	0.2221
Phantom Peak	50
Corr. Phantom Peak	0.2129
Argmin. Corr.	1500
Min. Corr.	0.1973
NSC	1.1258
RSC	1.5940

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	0.3478

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	0.1151
AUC	0.4945
CHANCE divergence	0.4215
Elbow Point	0.0000
JS Distance	0.7361
Synthetic AUC	0.5070
Synthetic Elbow Point	0.1740
Synthetic JS Distance	0.4564