Untitled

No description

Report generated at 2021-12-31 11:51:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88155058	147967716
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87498618	141073415
Mapped(QC-failed)	0	0
% Mapped	99.2600	95.3400
Paired	88155058	147967716
Paired(QC-failed)	0	0
Read1	44077529	73983858
Read1(QC-failed)	0	0
Read2	44077529	73983858
Read2(QC-failed)	0	0
Properly Paired	84555321	129978073
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9200	87.8400
With itself	87197982	139642816
With itself(QC-failed)	0	0
Singletons	300636	1430599
Singletons(QC-failed)	0	0
% Singleton	0.3400	0.9700
Diff. Chroms	2296445	4101665
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	39846422	58170389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	558702	1433825
Paired Opt. Dupes	2057	3355
% Dupes/100	0.0140	0.0246

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39831631	58124153
Distinct Read Pairs	39273919	56701457
One Read Pair	38730697	55332829
Two Read Pairs	529864	1333630
NRF = Distinct/Total	0.9860	0.9755
PBC1 = OnePair/Distinct	0.9862	0.9759
PBC2 = OnePair/TwoPair	73.0955	41.4904

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	78575440	113473128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78575440	113473128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78575440	113473128
Paired(QC-failed)	0	0
Read1	39287720	56736564
Read1(QC-failed)	0	0
Read2	39287720	56736564
Read2(QC-failed)	0	0
Properly Paired	78575440	113473128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78575440	113473128
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	230782
Np	0
N optimal	230782
N conservative	230782
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.	0.1922
Phantom Peak	55
Corr. Phantom Peak	0.1827
Argmin. Corr.	1500
Min. Corr.	0.1717
NSC	1.1195
RSC	1.8711

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	0.5481

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	0.1489
AUC	0.4954
CHANCE divergence	0.1709
Elbow Point	0.0000
JS Distance	0.7645
Synthetic AUC	0.5024
Synthetic Elbow Point	0.3688
Synthetic JS Distance	0.4886