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Report generated at 2022-09-03 00:21:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171938100	137088680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	163688297	134896264
Mapped(QC-failed)	0	0
% Mapped	95.2000	98.4000
Paired	171938100	137088680
Paired(QC-failed)	0	0
Read1	85969050	68544340
Read1(QC-failed)	0	0
Read2	85969050	68544340
Read2(QC-failed)	0	0
Properly Paired	162786582	134028989
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6800	97.7700
With itself	163188348	134480082
With itself(QC-failed)	0	0
Singletons	499949	416182
Singletons(QC-failed)	0	0
% Singleton	0.2900	0.3000
Diff. Chroms	106491	105917
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	73193609	59008108
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3712703	3208268
Paired Opt. Dupes	7741	16913
% Dupes/100	0.0507	0.0544

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	73193077	58974886
Distinct Read Pairs	69480415	55768361
One Read Pair	65938847	52823522
Two Read Pairs	3377695	2707860
NRF = Distinct/Total	0.9493	0.9456
PBC1 = OnePair/Distinct	0.9490	0.9472
PBC2 = OnePair/TwoPair	19.5218	19.5075

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	138961812	111599680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	138961812	111599680
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	138961812	111599680
Paired(QC-failed)	0	0
Read1	69480906	55799840
Read1(QC-failed)	0	0
Read2	69480906	55799840
Read2(QC-failed)	0	0
Properly Paired	138961812	111599680
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	138961812	111599680
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	161569
Np	0
N optimal	161569
N conservative	161569
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.	195
Corr. Est. Fragment Len.	0.2156
Phantom Peak	50
Corr. Phantom Peak	0.2144
Argmin. Corr.	1500
Min. Corr.	0.2007
NSC	1.0742
RSC	1.0856

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	0.4764

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	0.1612
AUC	0.4965
CHANCE divergence	0.1406
Elbow Point	0.0000
JS Distance	0.7442
Synthetic AUC	0.4997
Synthetic Elbow Point	0.3603
Synthetic JS Distance	0.4845