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Report generated at 2020-07-10 09:10:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123885920	172997562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117276028	170514341
Mapped(QC-failed)	0	0
% Mapped	94.6600	98.5600
Paired	123885920	172997562
Paired(QC-failed)	0	0
Read1	61942960	86498781
Read1(QC-failed)	0	0
Read2	61942960	86498781
Read2(QC-failed)	0	0
Properly Paired	114405288	165526176
Properly Paired(QC-failed)	0	0
% Properly Paired	92.3500	95.6800
With itself	116213459	169780024
With itself(QC-failed)	0	0
Singletons	1062569	734317
Singletons(QC-failed)	0	0
% Singleton	0.8600	0.4200
Diff. Chroms	169678	214733
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	43893513	72844563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2837220	589909
Paired Opt. Dupes	2689	3866
% Dupes/100	0.0646	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43830430	72728950
Distinct Read Pairs	41006733	72170728
One Read Pair	38425825	71649358
Two Read Pairs	2426521	508600
NRF = Distinct/Total	0.9356	0.9923
PBC1 = OnePair/Distinct	0.9371	0.9928
PBC2 = OnePair/TwoPair	15.8358	140.8757

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	82112586	144509308
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82112586	144509308
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82112586	144509308
Paired(QC-failed)	0	0
Read1	41056293	72254654
Read1(QC-failed)	0	0
Read2	41056293	72254654
Read2(QC-failed)	0	0
Properly Paired	82112586	144509308
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82112586	144509308
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	195137
Np	0
N optimal	195137
N conservative	195137
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.	115
Corr. Est. Fragment Len.	0.1859
Phantom Peak	50
Corr. Phantom Peak	0.2070
Argmin. Corr.	1500
Min. Corr.	0.1760
NSC	1.0564
RSC	0.3199

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	0.1743

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	0.2537
AUC	0.4955
CHANCE divergence	0.1054
Elbow Point	0.0000
JS Distance	0.6381
Synthetic AUC	0.4973
Synthetic Elbow Point	0.1926
Synthetic JS Distance	0.3205