Untitled

No description

Report generated at 2019-10-12 19:29:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77256764	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76015803	86768459
Mapped(QC-failed)	0	0
% Mapped	98.3900	97.7100
Paired	77256764	88801120
Paired(QC-failed)	0	0
Read1	38628382	44400560
Read1(QC-failed)	0	0
Read2	38628382	44400560
Read2(QC-failed)	0	0
Properly Paired	75623991	85806359
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8900	96.6300
With itself	75823102	86430737
With itself(QC-failed)	0	0
Singletons	192701	337722
Singletons(QC-failed)	0	0
% Singleton	0.2500	0.3800
Diff. Chroms	72045	102712
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	34916953	37886939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1821308	723026
Paired Opt. Dupes	4062	3740
% Dupes/100	0.0522	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34915555	37657060
Distinct Read Pairs	33094326	36953214
One Read Pair	31356216	36265585
Two Read Pairs	1658505	673617
NRF = Distinct/Total	0.9478	0.9813
PBC1 = OnePair/Distinct	0.9475	0.9814
PBC2 = OnePair/TwoPair	18.9063	53.8371

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	66191290	74327826
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66191290	74327826
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66191290	74327826
Paired(QC-failed)	0	0
Read1	33095645	37163913
Read1(QC-failed)	0	0
Read2	33095645	37163913
Read2(QC-failed)	0	0
Properly Paired	66191290	74327826
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66191290	74327826
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	187172
Np	0
N optimal	187172
N conservative	187172
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.	0.1742
Phantom Peak	50
Corr. Phantom Peak	0.1747
Argmin. Corr.	1500
Min. Corr.	0.1727
NSC	1.0090
RSC	0.7523

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	0.1633

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	0.2175
AUC	0.4950
CHANCE divergence	0.1707
Elbow Point	0.0000
JS Distance	0.6313
Synthetic AUC	0.5089
Synthetic Elbow Point	0.1835
Synthetic JS Distance	0.3552