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Report generated at 2022-01-07 21:57:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102129824	115662734
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100625497	113038251
Mapped(QC-failed)	0	0
% Mapped	98.5300	97.7300
Paired	102129824	115662734
Paired(QC-failed)	0	0
Read1	51064912	57831367
Read1(QC-failed)	0	0
Read2	51064912	57831367
Read2(QC-failed)	0	0
Properly Paired	91336532	109036939
Properly Paired(QC-failed)	0	0
% Properly Paired	89.4300	94.2700
With itself	99878350	112377816
With itself(QC-failed)	0	0
Singletons	747147	660435
Singletons(QC-failed)	0	0
% Singleton	0.7300	0.5700
Diff. Chroms	6914093	843986
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	42328872	48381997
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1071102	577446
Paired Opt. Dupes	1830	2513
% Dupes/100	0.0253	0.0119

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42271955	48321027
Distinct Read Pairs	41211940	47755668
One Read Pair	40179786	47208127
Two Read Pairs	1006404	537718
NRF = Distinct/Total	0.9749	0.9883
PBC1 = OnePair/Distinct	0.9750	0.9885
PBC2 = OnePair/TwoPair	39.9241	87.7935

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	82515540	95609102
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82515540	95609102
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82515540	95609102
Paired(QC-failed)	0	0
Read1	41257770	47804551
Read1(QC-failed)	0	0
Read2	41257770	47804551
Read2(QC-failed)	0	0
Properly Paired	82515540	95609102
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82515540	95609102
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	208217
Np	0
N optimal	208217
N conservative	208217
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.	0.1750
Phantom Peak	50
Corr. Phantom Peak	0.1725
Argmin. Corr.	1500
Min. Corr.	0.1676
NSC	1.0442
RSC	1.5157

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	0.2641

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	0.2490
AUC	0.4955
CHANCE divergence	0.1050
Elbow Point	0.0000
JS Distance	0.6727
Synthetic AUC	0.4999
Synthetic Elbow Point	0.1831
Synthetic JS Distance	0.3291