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Report generated at 2019-10-13 02:11:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129184402	74890440
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125877581	73000884
Mapped(QC-failed)	0	0
% Mapped	97.4400	97.4800
Paired	129184402	74890440
Paired(QC-failed)	0	0
Read1	64592201	37445220
Read1(QC-failed)	0	0
Read2	64592201	37445220
Read2(QC-failed)	0	0
Properly Paired	124423725	71988853
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3100	96.1300
With itself	124800018	72310070
With itself(QC-failed)	0	0
Singletons	1077563	690814
Singletons(QC-failed)	0	0
% Singleton	0.8300	0.9200
Diff. Chroms	99289	118954
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	55136594	31543148
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15459285	2120305
Paired Opt. Dupes	5403	2379
% Dupes/100	0.2804	0.0672

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55134855	31498588
Distinct Read Pairs	39676082	29382089
One Read Pair	29017651	27417596
Two Read Pairs	7333453	1823795
NRF = Distinct/Total	0.7196	0.9328
PBC1 = OnePair/Distinct	0.7314	0.9331
PBC2 = OnePair/TwoPair	3.9569	15.0333

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	79354618	58845686
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79354618	58845686
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79354618	58845686
Paired(QC-failed)	0	0
Read1	39677309	29422843
Read1(QC-failed)	0	0
Read2	39677309	29422843
Read2(QC-failed)	0	0
Properly Paired	79354618	58845686
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79354618	58845686
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	105360
Np	0
N optimal	105360
N conservative	105360
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.	140
Corr. Est. Fragment Len.	0.1667
Phantom Peak	50
Corr. Phantom Peak	0.1766
Argmin. Corr.	1500
Min. Corr.	0.1593
NSC	1.0465
RSC	0.4280

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	0.0907

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	0.2990
AUC	0.4954
CHANCE divergence	0.1043
Elbow Point	0.0000
JS Distance	0.5796
Synthetic AUC	0.5006
Synthetic Elbow Point	0.0829
Synthetic JS Distance	0.2477