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Report generated at 2021-06-17 10:31:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77718226	62446766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73874709	61444279
Mapped(QC-failed)	0	0
% Mapped	95.0500	98.3900
Paired	77718226	62446766
Paired(QC-failed)	0	0
Read1	38859113	31223383
Read1(QC-failed)	0	0
Read2	38859113	31223383
Read2(QC-failed)	0	0
Properly Paired	73370783	60211018
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4100	96.4200
With itself	73594838	61058927
With itself(QC-failed)	0	0
Singletons	279871	385352
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.6200
Diff. Chroms	26489	137146
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	33789135	25955256
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3441007	120864
Paired Opt. Dupes	38925	70313
% Dupes/100	0.1018	0.0047

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33787004	25953974
Distinct Read Pairs	30346219	25833113
One Read Pair	27300625	25714961
Two Read Pairs	2739090	116727
NRF = Distinct/Total	0.8982	0.9953
PBC1 = OnePair/Distinct	0.8996	0.9954
PBC2 = OnePair/TwoPair	9.9670	220.3000

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	60696256	51668784
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60696256	51668784
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60696256	51668784
Paired(QC-failed)	0	0
Read1	30348128	25834392
Read1(QC-failed)	0	0
Read2	30348128	25834392
Read2(QC-failed)	0	0
Properly Paired	60696256	51668784
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60696256	51668784
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	119769
Np	0
N optimal	119769
N conservative	119769
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.	0.2566
Phantom Peak	55
Corr. Phantom Peak	0.1845
Argmin. Corr.	1500
Min. Corr.	0.1527
NSC	1.6810
RSC	3.2612

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	0.4933

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	0.1405
AUC	0.4946
CHANCE divergence	0.1781
Elbow Point	0.0000
JS Distance	0.8205
Synthetic AUC	0.5036
Synthetic Elbow Point	0.3988
Synthetic JS Distance	0.5199