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Report generated at 2021-10-10 14:22:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	124473216	202126234
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117668442	198799328
Mapped(QC-failed)	0	0
% Mapped	94.5300	98.3500
Paired	124473216	202126234
Paired(QC-failed)	0	0
Read1	62236608	101063117
Read1(QC-failed)	0	0
Read2	62236608	101063117
Read2(QC-failed)	0	0
Properly Paired	114296757	176384044
Properly Paired(QC-failed)	0	0
% Properly Paired	91.8200	87.2600
With itself	115586360	196644255
With itself(QC-failed)	0	0
Singletons	2082082	2155073
Singletons(QC-failed)	0	0
% Singleton	1.6700	1.0700
Diff. Chroms	506115	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	46834774	72658135
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	33882189	9622785
Paired Opt. Dupes	8226	11648
% Dupes/100	0.7234	0.1324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46829108	72505168
Distinct Read Pairs	12950874	62908922
One Read Pair	3439963	54529901
Two Read Pairs	2323208	7308755
NRF = Distinct/Total	0.2766	0.8676
PBC1 = OnePair/Distinct	0.2656	0.8668
PBC2 = OnePair/TwoPair	1.4807	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	25905170	126070700
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	25905170	126070700
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	25905170	126070700
Paired(QC-failed)	0	0
Read1	12952585	63035350
Read1(QC-failed)	0	0
Read2	12952585	63035350
Read2(QC-failed)	0	0
Properly Paired	25905170	126070700
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	25905170	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	103097
Np	0
N optimal	103097
N conservative	103097
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.	160
Corr. Est. Fragment Len.	0.1182
Phantom Peak	50
Corr. Phantom Peak	0.1167
Argmin. Corr.	1500
Min. Corr.	0.1091
NSC	1.0838
RSC	1.1982

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	0.1321

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	0.2266
AUC	0.4902
CHANCE divergence	0.2119
Elbow Point	0.0000
JS Distance	0.6384
Synthetic AUC	0.5007
Synthetic Elbow Point	0.1868
Synthetic JS Distance	0.3011