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Report generated at 2019-11-01 12:34:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	134881426	226039766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132339990	215792208
Mapped(QC-failed)	0	0
% Mapped	98.1200	95.4700
Paired	134881426	226039766
Paired(QC-failed)	0	0
Read1	67440713	113019883
Read1(QC-failed)	0	0
Read2	67440713	113019883
Read2(QC-failed)	0	0
Properly Paired	129501021	149610145
Properly Paired(QC-failed)	0	0
% Properly Paired	96.0100	66.1900
With itself	131043541	208550392
With itself(QC-failed)	0	0
Singletons	1296449	7241816
Singletons(QC-failed)	0	0
% Singleton	0.9600	3.2000
Diff. Chroms	353421	32459107
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	50888757	41767173
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17856172	7918501
Paired Opt. Dupes	16684	11777
% Dupes/100	0.3509	0.1896

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50882020	41734528
Distinct Read Pairs	33028072	33823168
One Read Pair	20902163	27301386
Two Read Pairs	8064930	5377365
NRF = Distinct/Total	0.6491	0.8104
PBC1 = OnePair/Distinct	0.6329	0.8072
PBC2 = OnePair/TwoPair	2.5917	5.0771

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	66065170	67697344
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66065170	67697344
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66065170	67697344
Paired(QC-failed)	0	0
Read1	33032585	33848672
Read1(QC-failed)	0	0
Read2	33032585	33848672
Read2(QC-failed)	0	0
Properly Paired	66065170	67697344
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66065170	67697344
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	61899
Np	0
N optimal	61899
N conservative	61899
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.	0.1593
Phantom Peak	50
Corr. Phantom Peak	0.1834
Argmin. Corr.	1500
Min. Corr.	0.1539
NSC	1.0347
RSC	0.1816

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	0.0337

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	0.2920
AUC	0.4939
CHANCE divergence	0.1143
Elbow Point	0.0000
JS Distance	0.5468
Synthetic AUC	0.5112
Synthetic Elbow Point	0.0852
Synthetic JS Distance	0.2495