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Report generated at 2020-05-13 08:18:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56340330	61233540
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47088667	58236787
Mapped(QC-failed)	0	0
% Mapped	83.5800	95.1100
Paired	56340330	61233540
Paired(QC-failed)	0	0
Read1	28170165	30616770
Read1(QC-failed)	0	0
Read2	28170165	30616770
Read2(QC-failed)	0	0
Properly Paired	43811337	50526323
Properly Paired(QC-failed)	0	0
% Properly Paired	77.7600	82.5100
With itself	45509977	56771071
With itself(QC-failed)	0	0
Singletons	1578690	1465716
Singletons(QC-failed)	0	0
% Singleton	2.8000	2.3900
Diff. Chroms	1222949	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	19357215	21455327
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	283440	305205
Paired Opt. Dupes	1743	1806
% Dupes/100	0.0146	0.0142

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19354187	21407515
Distinct Read Pairs	19070794	21105831
One Read Pair	18790830	20807859
Two Read Pairs	276575	294314
NRF = Distinct/Total	0.9854	0.9859
PBC1 = OnePair/Distinct	0.9853	0.9859
PBC2 = OnePair/TwoPair	67.9412	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	38147550	42300244
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	38147550	42300244
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	38147550	42300244
Paired(QC-failed)	0	0
Read1	19073775	21150122
Read1(QC-failed)	0	0
Read2	19073775	21150122
Read2(QC-failed)	0	0
Properly Paired	38147550	42300244
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	38147550	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	109321
Np	0
N optimal	109321
N conservative	109321
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.	0.2013
Phantom Peak	50
Corr. Phantom Peak	0.1994
Argmin. Corr.	1500
Min. Corr.	0.1831
NSC	1.0994
RSC	1.1103

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	0.2703

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	0.1349
AUC	0.4933
CHANCE divergence	0.3912
Elbow Point	0.0000
JS Distance	0.7043
Synthetic AUC	0.5043
Synthetic Elbow Point	0.1524
Synthetic JS Distance	0.4144