Table 1 SEAseq quality metrics performed and their definitions
From: SEAseq: a portable and cloud-based chromatin occupancy analysis suite
Quality metric | Definition |
|---|---|
Aligned percent | Percentage of mapped reads |
Base quality | Per-base sequence quality distribution |
Estimated fragment width | Average fragment size of the peak distribution |
Estimated tag length | Sequencing read length |
Fraction of reads in peaks (FRiP) | The fraction of reads within coverage-enriched regions |
Linear stitched peaks (enhancers) | Total number of clustered enriched regions |
Non-redundant fraction (NRF) | Fraction of uniquely mapped sequencing reads |
Normalized peaksa | Peaks identified after input/control correction |
Normalized strand-correlation coefficient (NSC) | The ratio of the maximum cross-correlation value divided by the background cross-correction |
Sequence diversity | Sequence overrepresentation; if reads/sequences are overrepresented in the library |
PCR bottleneck coefficient (PBC) | It is a measure of library complexity determined by the fraction of genomic locations with exactly one unique read versus those covered by at least one unique read |
Peaks | Total number of enriched regions (peaks) |
Raw reads | Total number of sequencing reads |
Read lengthb | Average FASTQ read length |
Relative strand-correlation coefficient (RSC) | A strand cross-correlation ratio between the fragment-length cross-correlation and the read-length peak |
SE-like enriched regions (super enhancers) | Total number of SE-like clustered enriched regions |
Overall quality | Average score rank of all metrics calculated |