Hi all, sorry if this has been asked before but I wasn't able to find any threads related to this question.
While trying to annotate a fungal genome using RNA-seq, I've found that the program I use (Funannotate) will ignore/disregard/filter out transcripts on occasion, potentially because they don't look like a standard gene or for some other reason I'm not aware of. I've verified this by amplifying un-called genes from cDNA. What I would like to do is to be able to align every single transcript in a genomic region of interest to the reference genome, which sounds like something that should be possible with targeted sequencing (such as from Nanopore). However, I haven't found anything online about how to perform targeted RNA sequencing without already knowing what genes or transcripts I'm looking for.
Does anyone have any suggestions on how to move forward with this?
Thanks!
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