Figure 6.

Recall bar-plot versus isoform abundance in Set-up 1 for 100 bp-PE. Panels A (upper left) and B (upper right) depict recall bar-plots versus isoform abundance for the compared methods when the alignment is annotation driven, CA and IA case respectively. Panels C (bottom left) and D (bottom right) are analogous to Panels A and B, when the alignment is data driven. The figure refers to Set-up 1 and 100 bp-PE. Within each panel, the upper row represents the recall observed for lowly expressed isoforms, middle row for moderately expressed isoforms and bottom row for highly expressed isoforms; left column refers to methods used in Mode 1, middle column to methods used in Mode 2, right column to methods used in Mode 3. Different bars of the same colour for each method and mode of action correspond to the different depth (i.e., from left to right 0.25M, 0.5M, 1M, 5M, 10M and 20M). When the alignment is annotation driven, the same annotation provided during the alignment was used for Mode 1 and 2.

Angelini et al. BMC Bioinformatics 2014 15:135   doi:10.1186/1471-2105-15-135
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