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Fig. 1 | BMC Genomics

Fig. 1

From: LOGIQA: a database dedicated to long-range genome interactions quality assessment

Fig. 1

Principles in use for Quality Assessment. Total mapped paired-end tags (PETs) are first classified in intra-chromosomal and inter-chromosomal events. For quality assessment, only intra-chromosomal PETs spanning genome distances longer than 10 kb - referred here as filtered PETs - are considered. Random sub-sampling generates PET subsets corresponding to 90, 70 and 50 % of the original filtered PETs and the numbers of PETs in 5 kb or 25 kb size genomic windows is quantified. By comparing each of the PET counts/window in the various random subsets with that observed on the original dataset, the fraction of recovered PET counts (recPETs) after random sub-sampling and the dispersion from the theoretically expected values are calculated. Note that the expected values correspond to a decrease in the number of PET counts per window that is proportional to the random sub-sampling (e.g. recPETs/window =50 % when 50 % of filtered PETs are random sub-sampled). By evaluating the fraction of genomic windows with recPET count dispersions lower than a defined confidence interval (default value 10 %) global quality descriptors like the density and similarity quality indicators (denQCi, and simQCi respectively), as well as the global QCscore are computed. Overall these quality descriptors reflect the fractions of the observed long-range chromatin interactions (>10 kb), which are considered reproducible. On top of the panel: a chromatin interaction map derived from a HiC assay is depicted on the context of the observed PET counts (heatmap scale). On the bottom: After LOGIQA data treatment, the chromatin interaction map displays the inferred PET counts dispersion (in percent; heatmap scale). Notably, the bottom panel recapitulates the genomic contacts observed on the top panel, but in addition it provides a further information concerning their reproducibility over the multiple random sub-sampling assays accomplished during quality assessment

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