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Report generated at 2019-10-31 13:09:33

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	196827722	168079694
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	189483885	165646880
Mapped(QC-failed)	0	0
% Mapped	96.2700	98.5500
Paired	196827722	168079694
Paired(QC-failed)	0	0
Read1	98413861	84039847
Read1(QC-failed)	0	0
Read2	98413861	84039847
Read2(QC-failed)	0	0
Properly Paired	180891387	159505121
Properly Paired(QC-failed)	0	0
% Properly Paired	91.9000	94.9000
With itself	185888934	164126359
With itself(QC-failed)	0	0
Singletons	3594951	1520521
Singletons(QC-failed)	0	0
% Singleton	1.8300	0.9000
Diff. Chroms	1879609	2770169
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	59774991	66513677
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4925201	3909802
Paired Opt. Dupes	11227	10372
% Dupes/100	0.0824	0.0588

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59774330	66496808
Distinct Read Pairs	54849179	62587995
One Read Pair	50265167	58831025
Two Read Pairs	4272978	3612814
NRF = Distinct/Total	0.9176	0.9412
PBC1 = OnePair/Distinct	0.9164	0.9400
PBC2 = OnePair/TwoPair	11.7635	16.2840

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	109699580	125207750
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109699580	125207750
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	109699580	125207750
Paired(QC-failed)	0	0
Read1	54849790	62603875
Read1(QC-failed)	0	0
Read2	54849790	62603875
Read2(QC-failed)	0	0
Properly Paired	109699580	125207750
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	109699580	125207750
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	209650
Np	0
N optimal	209650
N conservative	209650
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.	125
Corr. Est. Fragment Len.	0.2062
Phantom Peak	50
Corr. Phantom Peak	0.2461
Argmin. Corr.	1500
Min. Corr.	0.1958
NSC	1.0532
RSC	0.2069

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	0.2463

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	0.2368
AUC	0.4952
CHANCE divergence	0.1074
Elbow Point	0.0000
JS Distance	0.6512
Synthetic AUC	0.5061
Synthetic Elbow Point	0.2225
Synthetic JS Distance	0.3501