QC Report


general
Report generated at2021-11-18 12:41:21
TitleENCSR816NWE-1
DescriptionNo description
Pipeline versionv1.10.0
Pipeline typeatac
Genomehg38
Alignerbowtie2
Sequencing endedness{'rep1': {'paired_end': True}}
Peak callermacs2

Alignment quality metrics


Fragment length statistics (filtered/deduped BAM)

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Fraction of reads in NFR0.5072226759325082
Fraction of reads in NFR (QC pass)True
Fraction of reads in NFR (QC reason)OK
NFR / mono-nuc reads1.398916905665799
NFR / mono-nuc reads (QC pass)False
NFR / mono-nuc reads (QC reason)out of range [2.5, inf]
Presence of NFR peakTrue
Presence of Mono-Nuc peakTrue
Presence of Di-Nuc peakTrue

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Open chromatin assays show distinct fragment length enrichments, as the cut sites are only in open chromatin and not in nucleosomes. As such, peaks representing different n-nucleosomal (ex mono-nucleosomal, di-nucleosomal) fragment lengths will arise. Good libraries will show these peaks in a fragment length distribution and will show specific peak ratios.



Sequence quality metrics (filtered/deduped BAM)

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Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.


Annotated genomic region enrichment

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Fraction of Reads in universal DHS regions0.34670473026301823
Fraction of Reads in blacklist regions0.005702649972217967
Fraction of Reads in promoter regions0.14959425701333515
Fraction of Reads in enhancer regions0.2904214150148414

Signal to noise can be assessed by considering whether reads are falling into known open regions (such as DHS regions) or not. A high fraction of reads should fall into the universal (across cell type) DHS set. A small fraction should fall into the blacklist regions. A high set (though not all) should fall into the promoter regions. A high set (though not all) should fall into the enhancer regions. The promoter regions should not take up all reads, as it is known that there is a bias for promoters in open chromatin assays.


Replication quality metrics


Number of raw peaks

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Number of peaks298761

Top 300000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics


Peak region size

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Min size150.0
25 percentile264.0
50 percentile (median)461.0
75 percentile834.0
Max size3358.0
Mean611.3665873390436

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Enrichment / Signal-to-noise ratio


Jensen-Shannon distance (filtered/deduped BAM)

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AUC0.2424696244953901
Synthetic AUC0.4967534477340894
X-intercept0.11482564823349001
Synthetic X-intercept0.0
Elbow Point0.7114503755745581
Synthetic Elbow Point0.5045355549220971
Synthetic JS Distance0.36285564792785097

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

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Fraction of Reads in Peaks0.26018061575599394

For macs2 raw peaks:


For overlap/IDR peaks: