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Report generated at 2020-07-09 21:11:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	62826802	172997562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58981490	170514341
Mapped(QC-failed)	0	0
% Mapped	93.8800	98.5600
Paired	62826802	172997562
Paired(QC-failed)	0	0
Read1	31413401	86498781
Read1(QC-failed)	0	0
Read2	31413401	86498781
Read2(QC-failed)	0	0
Properly Paired	58495635	165526176
Properly Paired(QC-failed)	0	0
% Properly Paired	93.1100	95.6800
With itself	58768795	169780024
With itself(QC-failed)	0	0
Singletons	212695	734317
Singletons(QC-failed)	0	0
% Singleton	0.3400	0.4200
Diff. Chroms	24919	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	27035094	72844563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3087543	589909
Paired Opt. Dupes	1127	3866
% Dupes/100	0.1142	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26965031	72728950
Distinct Read Pairs	23891472	72170728
One Read Pair	21220422	71649358
Two Read Pairs	2372651	508600
NRF = Distinct/Total	0.8860	0.9923
PBC1 = OnePair/Distinct	0.8882	0.9928
PBC2 = OnePair/TwoPair	8.9438	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	47895102	144509308
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47895102	144509308
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	47895102	144509308
Paired(QC-failed)	0	0
Read1	23947551	72254654
Read1(QC-failed)	0	0
Read2	23947551	72254654
Read2(QC-failed)	0	0
Properly Paired	47895102	144509308
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	47895102	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	92257
Np	0
N optimal	92257
N conservative	92257
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.	150
Corr. Est. Fragment Len.	0.2511
Phantom Peak	55
Corr. Phantom Peak	0.1984
Argmin. Corr.	1500
Min. Corr.	0.1526
NSC	1.6449
RSC	2.1507

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	0.4498

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	0.1538
AUC	0.4941
CHANCE divergence	0.1783
Elbow Point	0.0000
JS Distance	0.7967
Synthetic AUC	0.4987
Synthetic Elbow Point	0.4146
Synthetic JS Distance	0.4947