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Report generated at 2019-10-26 12:14:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122802738	265917970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115544581	247468185
Mapped(QC-failed)	0	0
% Mapped	94.0900	93.0600
Paired	122802738	265917970
Paired(QC-failed)	0	0
Read1	61401369	132958985
Read1(QC-failed)	0	0
Read2	61401369	132958985
Read2(QC-failed)	0	0
Properly Paired	109025959	230014508
Properly Paired(QC-failed)	0	0
% Properly Paired	88.7800	86.5000
With itself	110206116	235762666
With itself(QC-failed)	0	0
Singletons	5338465	11705519
Singletons(QC-failed)	0	0
% Singleton	4.3500	4.4000
Diff. Chroms	251758	1000428
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	41554366	94715746
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	21676320	28466270
Paired Opt. Dupes	3550	5233
% Dupes/100	0.5216	0.3005

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41552219	94356916
Distinct Read Pairs	19876952	66005399
One Read Pair	8666414	44764253
Two Read Pairs	5377461	15674972
NRF = Distinct/Total	0.4784	0.6995
PBC1 = OnePair/Distinct	0.4360	0.6782
PBC2 = OnePair/TwoPair	1.6116	2.8558

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	39756092	132498952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39756092	132498952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	39756092	132498952
Paired(QC-failed)	0	0
Read1	19878046	66249476
Read1(QC-failed)	0	0
Read2	19878046	66249476
Read2(QC-failed)	0	0
Properly Paired	39756092	132498952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	39756092	132498952
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	26848
Np	0
N optimal	26848
N conservative	26848
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.	120
Corr. Est. Fragment Len.	0.1389
Phantom Peak	50
Corr. Phantom Peak	0.1597
Argmin. Corr.	1500
Min. Corr.	0.1335
NSC	1.0407
RSC	0.2078

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	0.0189

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	0.2869
AUC	0.4921
CHANCE divergence	0.1303
Elbow Point	0.0000
JS Distance	0.5532
Synthetic AUC	0.5093
Synthetic Elbow Point	0.0827
Synthetic JS Distance	0.2426