Untitled

No description

Report generated at 2021-10-10 12:59:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	110992550	202126234
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103467389	198799328
Mapped(QC-failed)	0	0
% Mapped	93.2200	98.3500
Paired	110992550	202126234
Paired(QC-failed)	0	0
Read1	55496275	101063117
Read1(QC-failed)	0	0
Read2	55496275	101063117
Read2(QC-failed)	0	0
Properly Paired	99878697	176384044
Properly Paired(QC-failed)	0	0
% Properly Paired	89.9900	87.2600
With itself	101179634	196644255
With itself(QC-failed)	0	0
Singletons	2287755	2155073
Singletons(QC-failed)	0	0
% Singleton	2.0600	1.0700
Diff. Chroms	411907	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	41405308	72658135
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	31877276	9622785
Paired Opt. Dupes	7959	11648
% Dupes/100	0.7699	0.1324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41399580	72505168
Distinct Read Pairs	9526489	62908922
One Read Pair	2257021	54529901
Two Read Pairs	1455563	7308755
NRF = Distinct/Total	0.2301	0.8676
PBC1 = OnePair/Distinct	0.2369	0.8668
PBC2 = OnePair/TwoPair	1.5506	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	19056064	126070700
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	19056064	126070700
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	19056064	126070700
Paired(QC-failed)	0	0
Read1	9528032	63035350
Read1(QC-failed)	0	0
Read2	9528032	63035350
Read2(QC-failed)	0	0
Properly Paired	19056064	126070700
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	19056064	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	52465
Np	0
N optimal	52465
N conservative	52465
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.	185
Corr. Est. Fragment Len.	0.1003
Phantom Peak	50
Corr. Phantom Peak	0.0978
Argmin. Corr.	1500
Min. Corr.	0.0901
NSC	1.1129
RSC	1.3332

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	0.0524

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	0.2301
AUC	0.4886
CHANCE divergence	0.2517
Elbow Point	0.0000
JS Distance	0.6137
Synthetic AUC	0.5033
Synthetic Elbow Point	0.1482
Synthetic JS Distance	0.2645