I recently de-novo assembled a non-model fungal genome using PacBio and Illumina reads, but now we have new RNA-seq data that needs to be assembled. I figured the best way to assemble the transcriptome would be to use a genome guided assembler like Trinity...unless you guys recommend a different assembler and/or a different approach. Also, I have the genome as both a masked, and unmasked assembly, so which one would be best to use for assembling the transcriptome?
Thanks in advance! Morgan