Untitled

No description

Report generated at 2019-11-04 09:43:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	162018466	194166736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	153441119	188427054
Mapped(QC-failed)	0	0
% Mapped	94.7100	97.0400
Paired	162018466	194166736
Paired(QC-failed)	0	0
Read1	81009233	97083368
Read1(QC-failed)	0	0
Read2	81009233	97083368
Read2(QC-failed)	0	0
Properly Paired	149204816	183258385
Properly Paired(QC-failed)	0	0
% Properly Paired	92.0900	94.3800
With itself	151455819	186937146
With itself(QC-failed)	0	0
Singletons	1985300	1489908
Singletons(QC-failed)	0	0
% Singleton	1.2300	0.7700
Diff. Chroms	332780	1235264
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	56194758	80987770
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2479751	1179794
Paired Opt. Dupes	7907	10644
% Dupes/100	0.0441	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56193696	80909491
Distinct Read Pairs	53713993	79732095
One Read Pair	51335618	78571982
Two Read Pairs	2286964	1145607
NRF = Distinct/Total	0.9559	0.9854
PBC1 = OnePair/Distinct	0.9557	0.9855
PBC2 = OnePair/TwoPair	22.4471	68.5855

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	107430014	159615952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107430014	159615952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	107430014	159615952
Paired(QC-failed)	0	0
Read1	53715007	79807976
Read1(QC-failed)	0	0
Read2	53715007	79807976
Read2(QC-failed)	0	0
Properly Paired	107430014	159615952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	107430014	159615952
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	234302
Np	0
N optimal	234302
N conservative	234302
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.	0.2082
Phantom Peak	50
Corr. Phantom Peak	0.2515
Argmin. Corr.	1500
Min. Corr.	0.1987
NSC	1.0477
RSC	0.1795

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	0.3502

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	0.1992
AUC	0.4961
CHANCE divergence	0.1266
Elbow Point	0.0000
JS Distance	0.6970
Synthetic AUC	0.5070
Synthetic Elbow Point	0.2924
Synthetic JS Distance	0.4112