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. 2019 Jul 15;47(14):7262–7275. doi: 10.1093/nar/gkz599

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Graph visualization of simulated data. Artificial transcript models representing two splice variants of a 10 exon gene were generated (bottom). When combined together, the two simulated transcripts incorporated an alternative start site (E1a, E1b), mutually exclusive exons (E3a, E3b), a skipped exon (E5) and an alternative 5′ donor site (20 bp shorter E7). Two levels of sequencing depth/transcript abundance were simulated, so as to provide a total of 500 or 2000 125 bp reads for the combined transcript models. RNA assembly graphs were then generated using a percentage similarity threshold of p = 98 and three settings for the threshold for the length of similarity (l = 20, 40, 80). The resultant graphs were visualized Graphia Professional using a 2D layout. Graphs are laid out in 2D and node colours represent the exon to which they map.