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Report generated at 2020-05-14 19:35:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	55192792	144095950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52784963	133456854
Mapped(QC-failed)	0	0
% Mapped	95.6400	92.6200
Paired	55192792	144095950
Paired(QC-failed)	0	0
Read1	27596396	72047975
Read1(QC-failed)	0	0
Read2	27596396	72047975
Read2(QC-failed)	0	0
Properly Paired	51279365	100085786
Properly Paired(QC-failed)	0	0
% Properly Paired	92.9100	69.4600
With itself	52219819	127614780
With itself(QC-failed)	0	0
Singletons	565144	5842074
Singletons(QC-failed)	0	0
% Singleton	1.0200	4.0500
Diff. Chroms	628901	21841128
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	23134517	33283608
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	193462	401960
Paired Opt. Dupes	528	902
% Dupes/100	0.0084	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23118526	33264694
Distinct Read Pairs	22925213	32863263
One Read Pair	22733454	32466574
Two Read Pairs	190216	392011
NRF = Distinct/Total	0.9916	0.9879
PBC1 = OnePair/Distinct	0.9916	0.9879
PBC2 = OnePair/TwoPair	119.5139	82.8206

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	45882110	65763296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45882110	65763296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45882110	65763296
Paired(QC-failed)	0	0
Read1	22941055	32881648
Read1(QC-failed)	0	0
Read2	22941055	32881648
Read2(QC-failed)	0	0
Properly Paired	45882110	65763296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45882110	65763296
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	25524
Np	0
N optimal	25524
N conservative	25524
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.	205
Corr. Est. Fragment Len.	0.4823
Phantom Peak	55
Corr. Phantom Peak	0.4224
Argmin. Corr.	1500
Min. Corr.	0.1700
NSC	2.8374
RSC	1.2372

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	0.6088

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	0.0741
AUC	0.4940
CHANCE divergence	0.3707
Elbow Point	0.0000
JS Distance	0.8703
Synthetic AUC	0.4983
Synthetic Elbow Point	0.5060
Synthetic JS Distance	0.6369