Fig. 4.

Example of Needle’s workflow for (4, 4)-minimizers. The q-quantitative filter is constructed by determining all minimizers and their occurrences. A minimizer z with count c is added to level i if $t_i<c\le t_{i+1}$. For example, minimizer ‘ACCG’ occurs six times in the red file and is stored in the second level, because $t_2=4<=6<t_3=8$. Note that the dots in the otherwise empty levels represent minimizers not shown in the small excerpt of the RNA Seq files. The query transcript consists of 17 nucleotides and has 14 minimizers. If half of that (7) are found for any color, the transcript’s expression is estimated. For the red example, this happens on the first level. For the blue example, on the eighth level (because this is the last level, the expression is set to the threshold of that level) and, for the green example, on the seventh level (A color version of this figure appears in the online version of this article.)