Untitled

No description

Report generated at 2021-02-05 15:06:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	50415032	128405074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49855771	126457897
Mapped(QC-failed)	0	0
% Mapped	98.8900	98.4800
Paired	50415032	128405074
Paired(QC-failed)	0	0
Read1	25207516	64202537
Read1(QC-failed)	0	0
Read2	25207516	64202537
Read2(QC-failed)	0	0
Properly Paired	49333977	122387045
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8600	95.3100
With itself	49563966	125508177
With itself(QC-failed)	0	0
Singletons	291805	949720
Singletons(QC-failed)	0	0
% Singleton	0.5800	0.7400
Diff. Chroms	34354	158656
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	21964747	53542620
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	199987	280947
Paired Opt. Dupes	3899	2697
% Dupes/100	0.0091	0.0052

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21700752	53433746
Distinct Read Pairs	21560769	53172146
One Read Pair	21422491	52921658
Two Read Pairs	136709	245876
NRF = Distinct/Total	0.9935	0.9951
PBC1 = OnePair/Distinct	0.9936	0.9953
PBC2 = OnePair/TwoPair	156.7014	215.2372

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	43529520	106523346
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43529520	106523346
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	43529520	106523346
Paired(QC-failed)	0	0
Read1	21764760	53261673
Read1(QC-failed)	0	0
Read2	21764760	53261673
Read2(QC-failed)	0	0
Properly Paired	43529520	106523346
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	43529520	106523346
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	57020
Np	0
N optimal	57020
N conservative	57020
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.	150
Corr. Est. Fragment Len.	0.1817
Phantom Peak	50
Corr. Phantom Peak	0.1795
Argmin. Corr.	1500
Min. Corr.	0.1674
NSC	1.0852
RSC	1.1858

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	0.1566

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	0.2619
AUC	0.4936
CHANCE divergence	0.1219
Elbow Point	0.0000
JS Distance	0.6271
Synthetic AUC	0.5057
Synthetic Elbow Point	0.1893
Synthetic JS Distance	0.3130