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Report generated at 2022-01-07 13:26:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	111137116	32633358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110114304	32017375
Mapped(QC-failed)	0	0
% Mapped	99.0800	98.1100
Paired	111137116	32633358
Paired(QC-failed)	0	0
Read1	55568558	16316679
Read1(QC-failed)	0	0
Read2	55568558	16316679
Read2(QC-failed)	0	0
Properly Paired	109400720	31194037
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4400	95.5900
With itself	109800038	31710601
With itself(QC-failed)	0	0
Singletons	314266	306774
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.9400
Diff. Chroms	97458	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	49912626	13749916
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1573011	466098
Paired Opt. Dupes	3147	702
% Dupes/100	0.0315	0.0339

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49863179	13728708
Distinct Read Pairs	48298580	13265289
One Read Pair	46782181	12815823
Two Read Pairs	1472916	436590
NRF = Distinct/Total	0.9686	0.9662
PBC1 = OnePair/Distinct	0.9686	0.9661
PBC2 = OnePair/TwoPair	31.7616	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	96679230	26567636
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96679230	26567636
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	96679230	26567636
Paired(QC-failed)	0	0
Read1	48339615	13283818
Read1(QC-failed)	0	0
Read2	48339615	13283818
Read2(QC-failed)	0	0
Properly Paired	96679230	26567636
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	96679230	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	51297
Np	0
N optimal	51297
N conservative	51297
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.	0.1727
Phantom Peak	50
Corr. Phantom Peak	0.1719
Argmin. Corr.	1500
Min. Corr.	0.1664
NSC	1.0377
RSC	1.1273

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	0.0392

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	0.2963
AUC	0.4959
CHANCE divergence	0.0987
Elbow Point	0.0000
JS Distance	0.5925
Synthetic AUC	0.5045
Synthetic Elbow Point	0.0753
Synthetic JS Distance	0.2543