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Report generated at 2022-09-03 00:32:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	161517324	50889240
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	149675335	50058651
Mapped(QC-failed)	0	0
% Mapped	92.6700	98.3700
Paired	161517324	50889240
Paired(QC-failed)	0	0
Read1	80758662	25444620
Read1(QC-failed)	0	0
Read2	80758662	25444620
Read2(QC-failed)	0	0
Properly Paired	147472753	49717706
Properly Paired(QC-failed)	0	0
% Properly Paired	91.3000	97.7000
With itself	148639864	49906072
With itself(QC-failed)	0	0
Singletons	1035471	152579
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.3000
Diff. Chroms	153386	67298
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	62425917	22060886
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1714920	95014
Paired Opt. Dupes	8409	6064
% Dupes/100	0.0275	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62423445	22024154
Distinct Read Pairs	60708590	21929940
One Read Pair	59055077	21836362
Two Read Pairs	1600434	93000
NRF = Distinct/Total	0.9725	0.9957
PBC1 = OnePair/Distinct	0.9728	0.9957
PBC2 = OnePair/TwoPair	36.8994	234.7996

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	121421994	43931744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121421994	43931744
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	121421994	43931744
Paired(QC-failed)	0	0
Read1	60710997	21965872
Read1(QC-failed)	0	0
Read2	60710997	21965872
Read2(QC-failed)	0	0
Properly Paired	121421994	43931744
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	121421994	43931744
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	27119
Np	0
N optimal	27119
N conservative	27119
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.	115
Corr. Est. Fragment Len.	0.1814
Phantom Peak	50
Corr. Phantom Peak	0.2105
Argmin. Corr.	1500
Min. Corr.	0.1732
NSC	1.0471
RSC	0.2189

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	0.0150

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	0.3153
AUC	0.4963
CHANCE divergence	0.1009
Elbow Point	0.0000
JS Distance	0.5355
Synthetic AUC	0.5064
Synthetic Elbow Point	0.0302
Synthetic JS Distance	0.2256