Untitled

No description

Report generated at 2019-11-03 05:48:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115968904	158940554
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113755087	157152767
Mapped(QC-failed)	0	0
% Mapped	98.0900	98.8800
Paired	115968904	158940554
Paired(QC-failed)	0	0
Read1	57984452	79470277
Read1(QC-failed)	0	0
Read2	57984452	79470277
Read2(QC-failed)	0	0
Properly Paired	112063061	154442853
Properly Paired(QC-failed)	0	0
% Properly Paired	96.6300	97.1700
With itself	113357739	156399332
With itself(QC-failed)	0	0
Singletons	397348	753435
Singletons(QC-failed)	0	0
% Singleton	0.3400	0.4700
Diff. Chroms	883994	1218211
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	51173718	68222921
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11019177	2746068
Paired Opt. Dupes	17963	28097
% Dupes/100	0.2153	0.0403

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51170248	68139154
Distinct Read Pairs	40151776	65397649
One Read Pair	31123973	62741963
Two Read Pairs	7343636	2573454
NRF = Distinct/Total	0.7847	0.9598
PBC1 = OnePair/Distinct	0.7752	0.9594
PBC2 = OnePair/TwoPair	4.2382	24.3804

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	80309082	130953706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80309082	130953706
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80309082	130953706
Paired(QC-failed)	0	0
Read1	40154541	65476853
Read1(QC-failed)	0	0
Read2	40154541	65476853
Read2(QC-failed)	0	0
Properly Paired	80309082	130953706
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80309082	130953706
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	73362
Np	0
N optimal	73362
N conservative	73362
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.	200
Corr. Est. Fragment Len.	0.1808
Phantom Peak	50
Corr. Phantom Peak	0.1833
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.0549
RSC	0.7893

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	0.4094

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	0.2072
AUC	0.4954
CHANCE divergence	0.1082
Elbow Point	0.0000
JS Distance	0.7911
Synthetic AUC	0.5066
Synthetic Elbow Point	0.3400
Synthetic JS Distance	0.4205