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Report generated at 2022-01-06 13:54:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129855582	135365502
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127230003	133317923
Mapped(QC-failed)	0	0
% Mapped	97.9800	98.4900
Paired	129855582	135365502
Paired(QC-failed)	0	0
Read1	64927791	67682751
Read1(QC-failed)	0	0
Read2	64927791	67682751
Read2(QC-failed)	0	0
Properly Paired	125820400	128953755
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8900	95.2600
With itself	126553344	132693635
With itself(QC-failed)	0	0
Singletons	676659	624288
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.4600
Diff. Chroms	70648	147654
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	53404486	56839130
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	690315	427070
Paired Opt. Dupes	3886	3620
% Dupes/100	0.0129	0.0075

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53320043	56788289
Distinct Read Pairs	52644404	56369250
One Read Pair	51994504	55975158
Two Read Pairs	637394	386103
NRF = Distinct/Total	0.9873	0.9926
PBC1 = OnePair/Distinct	0.9877	0.9930
PBC2 = OnePair/TwoPair	81.5736	144.9747

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	105428342	112824120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105428342	112824120
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105428342	112824120
Paired(QC-failed)	0	0
Read1	52714171	56412060
Read1(QC-failed)	0	0
Read2	52714171	56412060
Read2(QC-failed)	0	0
Properly Paired	105428342	112824120
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105428342	112824120
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	64618
Np	0
N optimal	64618
N conservative	64618
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.	-10
Corr. Est. Fragment Len.	0.1767
Phantom Peak	50
Corr. Phantom Peak	0.1884
Argmin. Corr.	1500
Min. Corr.	0.1712
NSC	1.0324
RSC	0.3223

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	0.0554

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	0.3183
AUC	0.4960
CHANCE divergence	0.0974
Elbow Point	0.0000
JS Distance	0.5437
Synthetic AUC	0.5001
Synthetic Elbow Point	0.0638
Synthetic JS Distance	0.2194