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Report generated at 2020-05-14 19:23:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115836390	91936088
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110327480	86108967
Mapped(QC-failed)	0	0
% Mapped	95.2400	93.6600
Paired	115836390	91936088
Paired(QC-failed)	0	0
Read1	57918195	45968044
Read1(QC-failed)	0	0
Read2	57918195	45968044
Read2(QC-failed)	0	0
Properly Paired	108506621	74610692
Properly Paired(QC-failed)	0	0
% Properly Paired	93.6700	81.1500
With itself	109419665	83414092
With itself(QC-failed)	0	0
Singletons	907815	2694875
Singletons(QC-failed)	0	0
% Singleton	0.7800	2.9300
Diff. Chroms	388874	6003117
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	45900347	28516779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	460347	321586
Paired Opt. Dupes	1155	641
% Dupes/100	0.0100	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45885897	28515658
Distinct Read Pairs	45425752	28194090
One Read Pair	44970268	27875944
Two Read Pairs	450865	314754
NRF = Distinct/Total	0.9900	0.9887
PBC1 = OnePair/Distinct	0.9900	0.9887
PBC2 = OnePair/TwoPair	99.7422	88.5642

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	90880000	56390386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90880000	56390386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	90880000	56390386
Paired(QC-failed)	0	0
Read1	45440000	28195193
Read1(QC-failed)	0	0
Read2	45440000	28195193
Read2(QC-failed)	0	0
Properly Paired	90880000	56390386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	90880000	56390386
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	225005
Np	0
N optimal	225005
N conservative	225005
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.	155
Corr. Est. Fragment Len.	0.1973
Phantom Peak	50
Corr. Phantom Peak	0.2118
Argmin. Corr.	1500
Min. Corr.	0.1847
NSC	1.0680
RSC	0.4643

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	0.1721

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	0.2122
AUC	0.4957
CHANCE divergence	0.1600
Elbow Point	0.0000
JS Distance	0.6411
Synthetic AUC	0.5007
Synthetic Elbow Point	0.1638
Synthetic JS Distance	0.3747