Untitled

No description

Report generated at 2019-10-26 14:24:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103823460	294654588
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102061258	290510210
Mapped(QC-failed)	0	0
% Mapped	98.3000	98.5900
Paired	103823460	294654588
Paired(QC-failed)	0	0
Read1	51911730	147327294
Read1(QC-failed)	0	0
Read2	51911730	147327294
Read2(QC-failed)	0	0
Properly Paired	100039620	281900859
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3600	95.6700
With itself	101158385	288529717
With itself(QC-failed)	0	0
Singletons	902873	1980493
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.6700
Diff. Chroms	323275	3476801
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	38948733	117328478
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15071172	14788109
Paired Opt. Dupes	13964	29230
% Dupes/100	0.3869	0.1260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38946490	117267661
Distinct Read Pairs	23876195	102488519
One Read Pair	14071754	89380125
Two Read Pairs	6192566	11628471
NRF = Distinct/Total	0.6131	0.8740
PBC1 = OnePair/Distinct	0.5894	0.8721
PBC2 = OnePair/TwoPair	2.2724	7.6863

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	47755122	205080738
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47755122	205080738
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	47755122	205080738
Paired(QC-failed)	0	0
Read1	23877561	102540369
Read1(QC-failed)	0	0
Read2	23877561	102540369
Read2(QC-failed)	0	0
Properly Paired	47755122	205080738
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	47755122	205080738
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	53301
Np	0
N optimal	53301
N conservative	53301
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.	110
Corr. Est. Fragment Len.	0.1508
Phantom Peak	50
Corr. Phantom Peak	0.1733
Argmin. Corr.	1500
Min. Corr.	0.1451
NSC	1.0393
RSC	0.2022

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	0.0298

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	0.2865
AUC	0.4928
CHANCE divergence	0.1251
Elbow Point	0.0000
JS Distance	0.5492
Synthetic AUC	0.5056
Synthetic Elbow Point	0.1218
Synthetic JS Distance	0.2490