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Report generated at 2020-06-05 15:27:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	136199438	55795332
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	133213403	53857089
Mapped(QC-failed)	0	0
% Mapped	97.8100	96.5300
Paired	136199438	55795332
Paired(QC-failed)	0	0
Read1	68099719	27897666
Read1(QC-failed)	0	0
Read2	68099719	27897666
Read2(QC-failed)	0	0
Properly Paired	131106862	52296480
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2600	93.7300
With itself	131445981	52480399
With itself(QC-failed)	0	0
Singletons	1767422	1376690
Singletons(QC-failed)	0	0
% Singleton	1.3000	2.4700
Diff. Chroms	90692	46059
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	58142902	22626428
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15723061	274417
Paired Opt. Dupes	4136	1375
% Dupes/100	0.2704	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58141943	22613174
Distinct Read Pairs	42419130	22338978
One Read Pair	31076818	22067977
Two Read Pairs	8132124	267891
NRF = Distinct/Total	0.7296	0.9879
PBC1 = OnePair/Distinct	0.7326	0.9879
PBC2 = OnePair/TwoPair	3.8215	82.3767

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	84839682	44704022
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84839682	44704022
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84839682	44704022
Paired(QC-failed)	0	0
Read1	42419841	22352011
Read1(QC-failed)	0	0
Read2	42419841	22352011
Read2(QC-failed)	0	0
Properly Paired	84839682	44704022
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84839682	44704022
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	132681
Np	0
N optimal	132681
N conservative	132681
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.	220
Corr. Est. Fragment Len.	0.1644
Phantom Peak	50
Corr. Phantom Peak	0.1696
Argmin. Corr.	1500
Min. Corr.	0.1595
NSC	1.0307
RSC	0.4866

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	0.0966

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	0.2772
AUC	0.4956
CHANCE divergence	0.1094
Elbow Point	0.0000
JS Distance	0.6192
Synthetic AUC	0.5000
Synthetic Elbow Point	0.0871
Synthetic JS Distance	0.2766