Untitled

No description

Report generated at 2020-05-21 17:48:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	219785976	199291734
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106786893	192758941
Mapped(QC-failed)	0	0
% Mapped	48.5900	96.7200
Paired	219785976	199291734
Paired(QC-failed)	0	0
Read1	109892988	99645867
Read1(QC-failed)	0	0
Read2	109892988	99645867
Read2(QC-failed)	0	0
Properly Paired	104199530	190351557
Properly Paired(QC-failed)	0	0
% Properly Paired	47.4100	95.5100
With itself	104796917	191591556
With itself(QC-failed)	0	0
Singletons	1989976	1167385
Singletons(QC-failed)	0	0
% Singleton	0.9100	0.5900
Diff. Chroms	153294	372346
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	45383371	82947353
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	890462	947217
Paired Opt. Dupes	1627	3959
% Dupes/100	0.0196	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45373751	82921397
Distinct Read Pairs	44483525	81974628
One Read Pair	43611169	81039698
Two Read Pairs	854900	923351
NRF = Distinct/Total	0.9804	0.9886
PBC1 = OnePair/Distinct	0.9804	0.9886
PBC2 = OnePair/TwoPair	51.0132	87.7669

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	88985818	164000272
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88985818	164000272
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	88985818	164000272
Paired(QC-failed)	0	0
Read1	44492909	82000136
Read1(QC-failed)	0	0
Read2	44492909	82000136
Read2(QC-failed)	0	0
Properly Paired	88985818	164000272
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	88985818	164000272
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	39043
Np	0
N optimal	39043
N conservative	39043
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.	155
Corr. Est. Fragment Len.	0.1743
Phantom Peak	50
Corr. Phantom Peak	0.2244
Argmin. Corr.	1500
Min. Corr.	0.1644
NSC	1.0602
RSC	0.1648

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	0.0640

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	0.2814
AUC	0.4957
CHANCE divergence	0.1036
Elbow Point	0.0000
JS Distance	0.5773
Synthetic AUC	0.5045
Synthetic Elbow Point	0.0734
Synthetic JS Distance	0.2813