Untitled

No description

Report generated at 2021-02-09 16:53:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72179908	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67139514	143500908
Mapped(QC-failed)	0	0
% Mapped	93.0200	96.7800
Paired	72179908	148269018
Paired(QC-failed)	0	0
Read1	36089954	74134509
Read1(QC-failed)	0	0
Read2	36089954	74134509
Read2(QC-failed)	0	0
Properly Paired	65572103	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	90.8500	94.5800
With itself	66042151	141622671
With itself(QC-failed)	0	0
Singletons	1097363	1878237
Singletons(QC-failed)	0	0
% Singleton	1.5200	1.2700
Diff. Chroms	229572	652729
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	28124018	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	997359	523701
Paired Opt. Dupes	901	14446
% Dupes/100	0.0355	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28080942	57674075
Distinct Read Pairs	27085734	57472830
One Read Pair	26132275	57272993
Two Read Pairs	913669	198503
NRF = Distinct/Total	0.9646	0.9965
PBC1 = OnePair/Distinct	0.9648	0.9965
PBC2 = OnePair/TwoPair	28.6015	288.5246

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	54253318	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54253318	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54253318	117133936
Paired(QC-failed)	0	0
Read1	27126659	58566968
Read1(QC-failed)	0	0
Read2	27126659	58566968
Read2(QC-failed)	0	0
Properly Paired	54253318	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54253318	117133936
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	86493
Np	0
N optimal	86493
N conservative	86493
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.	0.3476
Phantom Peak	55
Corr. Phantom Peak	0.2798
Argmin. Corr.	1500
Min. Corr.	0.1986
NSC	1.7501
RSC	1.8356

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	0.6083

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	0.0962
AUC	0.4944
CHANCE divergence	0.2647
Elbow Point	0.0000
JS Distance	0.8660
Synthetic AUC	0.4982
Synthetic Elbow Point	0.5138
Synthetic JS Distance	0.5939