Untitled

No description

Report generated at 2022-09-02 15:04:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75938612	137088680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75094828	134896264
Mapped(QC-failed)	0	0
% Mapped	98.8900	98.4000
Paired	75938612	137088680
Paired(QC-failed)	0	0
Read1	37969306	68544340
Read1(QC-failed)	0	0
Read2	37969306	68544340
Read2(QC-failed)	0	0
Properly Paired	74691182	134028989
Properly Paired(QC-failed)	0	0
% Properly Paired	98.3600	97.7700
With itself	74863216	134480082
With itself(QC-failed)	0	0
Singletons	231612	416182
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.3000
Diff. Chroms	55958	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	34813966	59008108
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1849888	3208268
Paired Opt. Dupes	2224	16913
% Dupes/100	0.0531	0.0544

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34813664	58974886
Distinct Read Pairs	32963799	55768361
One Read Pair	31199348	52823522
Two Read Pairs	1682570	2707860
NRF = Distinct/Total	0.9469	0.9456
PBC1 = OnePair/Distinct	0.9465	0.9472
PBC2 = OnePair/TwoPair	18.5427	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	65928156	111599680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65928156	111599680
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	65928156	111599680
Paired(QC-failed)	0	0
Read1	32964078	55799840
Read1(QC-failed)	0	0
Read2	32964078	55799840
Read2(QC-failed)	0	0
Properly Paired	65928156	111599680
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	65928156	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	97495
Np	0
N optimal	97495
N conservative	97495
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.	0.2605
Phantom Peak	55
Corr. Phantom Peak	0.2458
Argmin. Corr.	1500
Min. Corr.	0.1960
NSC	1.3293
RSC	1.2946

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	0.4687

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	0.1428
AUC	0.4950
CHANCE divergence	0.1888
Elbow Point	0.0000
JS Distance	0.7861
Synthetic AUC	0.5040
Synthetic Elbow Point	0.4063
Synthetic JS Distance	0.5093