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Report generated at 2020-06-06 13:09:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	179910574	124179460
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	178101642	119894833
Mapped(QC-failed)	0	0
% Mapped	98.9900	96.5500
Paired	179910574	124179460
Paired(QC-failed)	0	0
Read1	89955287	62089730
Read1(QC-failed)	0	0
Read2	89955287	62089730
Read2(QC-failed)	0	0
Properly Paired	177008082	116530232
Properly Paired(QC-failed)	0	0
% Properly Paired	98.3900	93.8400
With itself	177497343	116928558
With itself(QC-failed)	0	0
Singletons	604299	2966275
Singletons(QC-failed)	0	0
% Singleton	0.3400	2.3900
Diff. Chroms	142211	93046
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	79526578	50364137
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6043141	686746
Paired Opt. Dupes	4862	3030
% Dupes/100	0.0760	0.0136

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	79524511	50330806
Distinct Read Pairs	73481521	49644969
One Read Pair	67911119	48972551
Two Read Pairs	5134374	660986
NRF = Distinct/Total	0.9240	0.9864
PBC1 = OnePair/Distinct	0.9242	0.9865
PBC2 = OnePair/TwoPair	13.2268	74.0901

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	146966874	99354782
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	146966874	99354782
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	146966874	99354782
Paired(QC-failed)	0	0
Read1	73483437	49677391
Read1(QC-failed)	0	0
Read2	73483437	49677391
Read2(QC-failed)	0	0
Properly Paired	146966874	99354782
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	146966874	99354782
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	199886
Np	0
N optimal	199886
N conservative	199886
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.	135
Corr. Est. Fragment Len.	0.1746
Phantom Peak	50
Corr. Phantom Peak	0.1839
Argmin. Corr.	1500
Min. Corr.	0.1711
NSC	1.0206
RSC	0.2756

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	0.1070

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	0.2987
AUC	0.4966
CHANCE divergence	0.1025
Elbow Point	0.0000
JS Distance	0.6066
Synthetic AUC	0.4975
Synthetic Elbow Point	0.0773
Synthetic JS Distance	0.2475