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Report generated at 2022-09-03 00:55:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	153480010	65769896
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	141088278	64886900
Mapped(QC-failed)	0	0
% Mapped	91.9300	98.6600
Paired	153480010	65769896
Paired(QC-failed)	0	0
Read1	76740005	32884948
Read1(QC-failed)	0	0
Read2	76740005	32884948
Read2(QC-failed)	0	0
Properly Paired	138144216	64470476
Properly Paired(QC-failed)	0	0
% Properly Paired	90.0100	98.0200
With itself	139443352	64685111
With itself(QC-failed)	0	0
Singletons	1644926	201789
Singletons(QC-failed)	0	0
% Singleton	1.0700	0.3100
Diff. Chroms	149965	65977
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	50709609	28526999
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13191743	113439
Paired Opt. Dupes	5454	1566
% Dupes/100	0.2601	0.0040

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50707941	28513550
Distinct Read Pairs	37516637	28400237
One Read Pair	27344286	28288484
Two Read Pairs	7779848	110529
NRF = Distinct/Total	0.7399	0.9960
PBC1 = OnePair/Distinct	0.7289	0.9961
PBC2 = OnePair/TwoPair	3.5148	255.9372

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	75035732	56827120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75035732	56827120
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75035732	56827120
Paired(QC-failed)	0	0
Read1	37517866	28413560
Read1(QC-failed)	0	0
Read2	37517866	28413560
Read2(QC-failed)	0	0
Properly Paired	75035732	56827120
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75035732	56827120
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	193956
Np	0
N optimal	193956
N conservative	193956
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.	200
Corr. Est. Fragment Len.	0.1920
Phantom Peak	50
Corr. Phantom Peak	0.2353
Argmin. Corr.	1500
Min. Corr.	0.1808
NSC	1.0619
RSC	0.2057

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	0.2410

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	0.2090
AUC	0.4953
CHANCE divergence	0.1513
Elbow Point	0.0000
JS Distance	0.6525
Synthetic AUC	0.5024
Synthetic Elbow Point	0.2027
Synthetic JS Distance	0.3815