Is anyone familiar with the graph mapping analysis programs that can incorporate the new pangenome graph maps (I probably have my terminology wrong here). Specifically, I'm interested in knowing if any of the programs (or if it is even possible) to be able to align very short RNA-seq reads (i.e. MicroRNA sequence data) to a pangenome graph map? I'm having trouble trying to figure this out or find any good articles on it. Any information is appreciated
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I wish I could help with this, but I don't have any experience with pangenome work. I do feel like I've heard of something like this before. Maybe this pantranscriptomics paper (https://www.nature.com/articles/s41592-022-01731-9) is something closer to what you're looking for.
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
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