QC Report


general
Report generated at2021-11-17 13:12:04
TitleENCSR442RZO-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 NFR0.8825187217972925
Fraction of reads in NFR (QC pass)True
Fraction of reads in NFR (QC reason)OK
NFR / mono-nuc reads9.54296330902264
NFR / mono-nuc reads (QC pass)True
NFR / mono-nuc reads (QC reason)OK
Presence of NFR peakTrue
Presence of Mono-Nuc peakFalse
Presence of Di-Nuc peakFalse

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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 regions0.4418654158425298
Fraction of Reads in blacklist regions0.024310577087474007
Fraction of Reads in promoter regions0.1770674443707727
Fraction of Reads in enhancer regions0.3524338237601138

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 peaks298955

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 percentile378.0
50 percentile (median)637.0
75 percentile1013.0
Max size3587.0
Mean744.8284056128849

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Enrichment / Signal-to-noise ratio


Jensen-Shannon distance (filtered/deduped BAM)

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AUC0.202063802376644
Synthetic AUC0.4976942989297489
X-intercept0.11511978023296265
Synthetic X-intercept0.0
Elbow Point0.7609353694573402
Synthetic Elbow Point0.49966816576753287
Synthetic JS Distance0.43490866992197313

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

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Fraction of Reads in Peaks0.3560201130216089

For macs2 raw peaks:


For overlap/IDR peaks: