How did Dobin et al. create these figures?

Question

[helen]

I was wondering if anyone knew how Dobin et al. mined the plotted information in Figure 3 in the STAR paper?

These include Number of unannotated junctions, % of mapper-exclusive junctions and more plots on a x-axis of minimum number of reads per junctions?

Where did they find this information out when doing the RNAseq pipeline?

[Istvan Albert]

I would ask the authors for this information - unfortunately data distribution - especially intermediate data distribution, and that of showing the data that plots are relying on is not a priority

my guess is that they counted the reads that overlap with each exon junction coordinate. For example, using bedtools you could create 1 bp flanking regions for each exon then select all the alignments that overlap with these coordinates.