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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Regions not covered by long read in --mix mode #425

Closed ytomofuji closed 2 months ago

ytomofuji commented 2 months ago

Thank you for creating this amazing tool!

I have a question about the --mix mode in stringtie2. In Figure 1 of your paper (https://doi.org/10.1371/journal.pcbi.1009730), it was shown that --mix mode can assemble regions that are not covered by long reads but are covered by short reads. However,in the method section, it seems that long read data is used for constructing the splice graph. Are short read data also used in constructing the splice graph? Or are regions not included in the splice graph added during the assembly step?

I would greatly appreciate your help!

mpertea commented 2 months ago

Both short reads and long reads are used in the construction of the splice graph. The long reads, when present are used first to guide the path from source to sink in the graph.

ytomofuji commented 2 months ago

I understand! Thank you for your prompt response!