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Report generated at 2020-05-13 07:01:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	49428710	61233540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39084388	58236787
Mapped(QC-failed)	0	0
% Mapped	79.0700	95.1100
Paired	49428710	61233540
Paired(QC-failed)	0	0
Read1	24714355	30616770
Read1(QC-failed)	0	0
Read2	24714355	30616770
Read2(QC-failed)	0	0
Properly Paired	37047120	50526323
Properly Paired(QC-failed)	0	0
% Properly Paired	74.9500	82.5100
With itself	37906891	56771071
With itself(QC-failed)	0	0
Singletons	1177497	1465716
Singletons(QC-failed)	0	0
% Singleton	2.3800	2.3900
Diff. Chroms	476412	4278577
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	15876283	21455327
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	220776	305205
Paired Opt. Dupes	1356	1806
% Dupes/100	0.0139	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15871436	21407515
Distinct Read Pairs	15650755	21105831
One Read Pair	15432751	20807859
Two Read Pairs	215370	294314
NRF = Distinct/Total	0.9861	0.9859
PBC1 = OnePair/Distinct	0.9861	0.9859
PBC2 = OnePair/TwoPair	71.6569	70.6995

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	31311014	42300244
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	31311014	42300244
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	31311014	42300244
Paired(QC-failed)	0	0
Read1	15655507	21150122
Read1(QC-failed)	0	0
Read2	15655507	21150122
Read2(QC-failed)	0	0
Properly Paired	31311014	42300244
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	31311014	42300244
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	81756
Np	0
N optimal	81756
N conservative	81756
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.	260
Corr. Est. Fragment Len.	0.1946
Phantom Peak	50
Corr. Phantom Peak	0.1940
Argmin. Corr.	1500
Min. Corr.	0.1766
NSC	1.1019
RSC	1.0348

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	0.1158

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	0.1494
AUC	0.4927
CHANCE divergence	0.3977
Elbow Point	0.0000
JS Distance	0.6792
Synthetic AUC	0.5049
Synthetic Elbow Point	0.0803
Synthetic JS Distance	0.3714