Untitled

No description

Report generated at 2021-03-18 11:18:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	9874250	120326326
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	5148231	115169165
Mapped(QC-failed)	0	0
% Mapped	52.1400	95.7100
Paired	9874250	120326326
Paired(QC-failed)	0	0
Read1	4937125	60163163
Read1(QC-failed)	0	0
Read2	4937125	60163163
Read2(QC-failed)	0	0
Properly Paired	4901171	99959048
Properly Paired(QC-failed)	0	0
% Properly Paired	49.6400	83.0700
With itself	5095494	113514451
With itself(QC-failed)	0	0
Singletons	52737	1654714
Singletons(QC-failed)	0	0
% Singleton	0.5300	1.3800
Diff. Chroms	7651	8596702
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	2209372	44206103
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	201337	461681
Paired Opt. Dupes	416	1289
% Dupes/100	0.0911	0.0104

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	2206986	44178985
Distinct Read Pairs	2005890	43721013
One Read Pair	1820415	43278165
Two Read Pairs	171479	434626
NRF = Distinct/Total	0.9089	0.9896
PBC1 = OnePair/Distinct	0.9075	0.9899
PBC2 = OnePair/TwoPair	10.6160	99.5756

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	4016070	87488844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	4016070	87488844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	4016070	87488844
Paired(QC-failed)	0	0
Read1	2008035	43744422
Read1(QC-failed)	0	0
Read2	2008035	43744422
Read2(QC-failed)	0	0
Properly Paired	4016070	87488844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	4016070	87488844
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	75457
Np	0
N optimal	75457
N conservative	75457
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 (2M)

	rep1
Reads	2634375
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.0600
Phantom Peak	50
Corr. Phantom Peak	0.0429
Argmin. Corr.	1500
Min. Corr.	0.0329
NSC	1.8207
RSC	2.7194

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	0.2273

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	0.0881
AUC	0.4797
CHANCE divergence	0.7115
Elbow Point	0.0000
JS Distance	0.7418
Synthetic AUC	0.5162
Synthetic Elbow Point	0.1995
Synthetic JS Distance	0.2877