I typically run DE analyses through the trinity pipeline, but due to certain features of the transcriptome I'm currently working on, I've found it's essential to use a kmer value higher than allowed in trinity. I'm not used to the various software for doing DE analyses outside of trinity.
I am working with a de novo assembly from a non-model organism (2 genotypes) and I don't have a high quality genome assembly to go with it. I have carried out transcript-level abundance pseudoalignments with salmon, and I'd like to get gene-level abundances, but I'm not quite sure how to do this. It seems that tximport is commonly used to get this, but from all of the examples I've seen, it seems that it requires a known set of genes, presumably from a sequenced genome project.
Is it possible to do what I want to do with tximport? Or some other program?
Thanks for your help!