Untitled

No description

Report generated at 2019-10-13 09:01:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	85646856	100468200
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84100243	98722536
Mapped(QC-failed)	0	0
% Mapped	98.1900	98.2600
Paired	85646856	100468200
Paired(QC-failed)	0	0
Read1	42823428	50234100
Read1(QC-failed)	0	0
Read2	42823428	50234100
Read2(QC-failed)	0	0
Properly Paired	83295231	97581946
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2500	97.1300
With itself	83635012	98187762
With itself(QC-failed)	0	0
Singletons	465231	534774
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.5300
Diff. Chroms	106780	175930
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	36158214	42692718
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	480749	481852
Paired Opt. Dupes	5752	6941
% Dupes/100	0.0133	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36157168	42649523
Distinct Read Pairs	35676434	42168744
One Read Pair	35201968	41697848
Two Read Pairs	468497	463478
NRF = Distinct/Total	0.9867	0.9887
PBC1 = OnePair/Distinct	0.9867	0.9888
PBC2 = OnePair/TwoPair	75.1381	89.9673

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	71354930	84421732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71354930	84421732
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71354930	84421732
Paired(QC-failed)	0	0
Read1	35677465	42210866
Read1(QC-failed)	0	0
Read2	35677465	42210866
Read2(QC-failed)	0	0
Properly Paired	71354930	84421732
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71354930	84421732
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	37283
Np	0
N optimal	37283
N conservative	37283
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.	115
Corr. Est. Fragment Len.	0.1770
Phantom Peak	50
Corr. Phantom Peak	0.1905
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.0301
RSC	0.2776

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	0.0412

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	0.3205
AUC	0.4952
CHANCE divergence	0.1043
Elbow Point	0.0000
JS Distance	0.5237
Synthetic AUC	0.5085
Synthetic Elbow Point	0.0549
Synthetic JS Distance	0.2139