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Report generated at 2022-09-03 08:15:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	147806838	137088680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	141557358	134896264
Mapped(QC-failed)	0	0
% Mapped	95.7700	98.4000
Paired	147806838	137088680
Paired(QC-failed)	0	0
Read1	73903419	68544340
Read1(QC-failed)	0	0
Read2	73903419	68544340
Read2(QC-failed)	0	0
Properly Paired	139509581	134028989
Properly Paired(QC-failed)	0	0
% Properly Paired	94.3900	97.7700
With itself	140950839	134480082
With itself(QC-failed)	0	0
Singletons	606519	416182
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.3000
Diff. Chroms	171198	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	61791578	59008108
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3429080	3208268
Paired Opt. Dupes	7119	16913
% Dupes/100	0.0555	0.0544

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	61790253	58974886
Distinct Read Pairs	58361242	55768361
One Read Pair	55106770	52823522
Two Read Pairs	3088235	2707860
NRF = Distinct/Total	0.9445	0.9456
PBC1 = OnePair/Distinct	0.9442	0.9472
PBC2 = OnePair/TwoPair	17.8441	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	116724996	111599680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116724996	111599680
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	116724996	111599680
Paired(QC-failed)	0	0
Read1	58362498	55799840
Read1(QC-failed)	0	0
Read2	58362498	55799840
Read2(QC-failed)	0	0
Properly Paired	116724996	111599680
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	116724996	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	147565
Np	0
N optimal	147565
N conservative	147565
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.	145
Corr. Est. Fragment Len.	0.1780
Phantom Peak	50
Corr. Phantom Peak	0.1864
Argmin. Corr.	1500
Min. Corr.	0.1721
NSC	1.0342
RSC	0.4121

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	0.1953

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	0.2879
AUC	0.4962
CHANCE divergence	0.0963
Elbow Point	0.0000
JS Distance	0.6183
Synthetic AUC	0.4987
Synthetic Elbow Point	0.1358
Synthetic JS Distance	0.2760