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Report generated at 2021-10-10 12:24:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96447838	202126234
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91297438	198799328
Mapped(QC-failed)	0	0
% Mapped	94.6600	98.3500
Paired	96447838	202126234
Paired(QC-failed)	0	0
Read1	48223919	101063117
Read1(QC-failed)	0	0
Read2	48223919	101063117
Read2(QC-failed)	0	0
Properly Paired	88436977	176384044
Properly Paired(QC-failed)	0	0
% Properly Paired	91.6900	87.2600
With itself	90157123	196644255
With itself(QC-failed)	0	0
Singletons	1140315	2155073
Singletons(QC-failed)	0	0
% Singleton	1.1800	1.0700
Diff. Chroms	811281	15415697
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	36120106	72658135
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	18425882	9622785
Paired Opt. Dupes	6162	11648
% Dupes/100	0.5101	0.1324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36112755	72505168
Distinct Read Pairs	17690380	62908922
One Read Pair	8246586	54529901
Two Read Pairs	4577695	7308755
NRF = Distinct/Total	0.4899	0.8676
PBC1 = OnePair/Distinct	0.4662	0.8668
PBC2 = OnePair/TwoPair	1.8015	7.4609

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	35388448	126070700
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35388448	126070700
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	35388448	126070700
Paired(QC-failed)	0	0
Read1	17694224	63035350
Read1(QC-failed)	0	0
Read2	17694224	63035350
Read2(QC-failed)	0	0
Properly Paired	35388448	126070700
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	35388448	126070700
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	55481
Np	0
N optimal	55481
N conservative	55481
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.	165
Corr. Est. Fragment Len.	0.1424
Phantom Peak	50
Corr. Phantom Peak	0.1461
Argmin. Corr.	1500
Min. Corr.	0.1339
NSC	1.0640
RSC	0.7017

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	0.0631

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	0.2712
AUC	0.4916
CHANCE divergence	0.1464
Elbow Point	0.0000
JS Distance	0.5631
Synthetic AUC	0.4953
Synthetic Elbow Point	0.1363
Synthetic JS Distance	0.2616