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Fig. 2 | BMC Genomics

Fig. 2

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

Fig. 2

Assessing quality descriptors over long-range genome interaction assays. a Scatter-plot illustrating the fraction of PET counts recovered after random subsampling (Y-axis) relative to the original PET counts in 5 kb genome windows (X-axis). Note that genome windows with high PET counts contain PET levels close to the expected value; in contrast, the lower the PET counts, the higher is the deviation from this theoretically expected level. b Recovery scatter-plots assessed from datasets with increasing PET count levels (from 100 to 500 millions). Note that we generated these datasets by random sub-sampling of a large metafile (>600 million reads). c QCscores computed from datasets presenting increasing PET count levels (from 100 to 500 millions). The illustrated QCscores, computed from five independent replicates, present variation coefficients below 3 % (see Additional file 1: Figure S2). d Local displays illustrating chromatin interactions (chromosome 6, mm9) evaluated in the context of PET count dispersion levels (percentage) per genomic window (5 kb) relative to the expected recovery levels. Note that short-range genomic interactions (diagonal) show the lowest dispersion levels

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