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Report generated at 2020-07-09 13:06:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81430974	99982538
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73700752	98422018
Mapped(QC-failed)	0	0
% Mapped	90.5100	98.4400
Paired	81430974	99982538
Paired(QC-failed)	0	0
Read1	40715487	49991269
Read1(QC-failed)	0	0
Read2	40715487	49991269
Read2(QC-failed)	0	0
Properly Paired	72832778	95501110
Properly Paired(QC-failed)	0	0
% Properly Paired	89.4400	95.5200
With itself	73340090	97903435
With itself(QC-failed)	0	0
Singletons	360662	518583
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5200
Diff. Chroms	26092	131000
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	33599269	42065303
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4997411	256391
Paired Opt. Dupes	3302	2694
% Dupes/100	0.1487	0.0061

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33591969	42050526
Distinct Read Pairs	28595795	41795152
One Read Pair	24282446	41551531
Two Read Pairs	3754155	239437
NRF = Distinct/Total	0.8513	0.9939
PBC1 = OnePair/Distinct	0.8492	0.9942
PBC2 = OnePair/TwoPair	6.4682	173.5385

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	57203716	83617824
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57203716	83617824
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57203716	83617824
Paired(QC-failed)	0	0
Read1	28601858	41808912
Read1(QC-failed)	0	0
Read2	28601858	41808912
Read2(QC-failed)	0	0
Properly Paired	57203716	83617824
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57203716	83617824
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	122969
Np	0
N optimal	122969
N conservative	122969
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.	150
Corr. Est. Fragment Len.	0.2059
Phantom Peak	55
Corr. Phantom Peak	0.1751
Argmin. Corr.	1500
Min. Corr.	0.1555
NSC	1.3238
RSC	2.5731

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	0.3643

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	0.1964
AUC	0.4946
CHANCE divergence	0.1320
Elbow Point	0.0000
JS Distance	0.7529
Synthetic AUC	0.5041
Synthetic Elbow Point	0.3161
Synthetic JS Distance	0.4246