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Report generated at 2021-12-31 14:44:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	112859992	32633358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105351663	32017375
Mapped(QC-failed)	0	0
% Mapped	93.3500	98.1100
Paired	112859992	32633358
Paired(QC-failed)	0	0
Read1	56429996	16316679
Read1(QC-failed)	0	0
Read2	56429996	16316679
Read2(QC-failed)	0	0
Properly Paired	97918468	31194037
Properly Paired(QC-failed)	0	0
% Properly Paired	86.7600	95.5900
With itself	104113856	31710601
With itself(QC-failed)	0	0
Singletons	1237807	306774
Singletons(QC-failed)	0	0
% Singleton	1.1000	0.9400
Diff. Chroms	151973	307689
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	44363227	13749916
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4230565	466098
Paired Opt. Dupes	429	702
% Dupes/100	0.0954	0.0339

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44219059	13728708
Distinct Read Pairs	40036938	13265289
One Read Pair	36272495	12815823
Two Read Pairs	3422512	436590
NRF = Distinct/Total	0.9054	0.9662
PBC1 = OnePair/Distinct	0.9060	0.9661
PBC2 = OnePair/TwoPair	10.5982	29.3544

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	80265324	26567636
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80265324	26567636
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80265324	26567636
Paired(QC-failed)	0	0
Read1	40132662	13283818
Read1(QC-failed)	0	0
Read2	40132662	13283818
Read2(QC-failed)	0	0
Properly Paired	80265324	26567636
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80265324	26567636
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	52933
Np	0
N optimal	52933
N conservative	52933
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.	145
Corr. Est. Fragment Len.	0.1943
Phantom Peak	50
Corr. Phantom Peak	0.1830
Argmin. Corr.	1500
Min. Corr.	0.1611
NSC	1.2066
RSC	1.5143

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	0.2106

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	0.2588
AUC	0.4955
CHANCE divergence	0.0992
Elbow Point	0.0000
JS Distance	0.6800
Synthetic AUC	0.5042
Synthetic Elbow Point	0.2038
Synthetic JS Distance	0.3484