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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