I am working on an RNA seq project with non model organisms, where I am hoping to discover the differential expression of a specific set of genes and/or sequence variants of the genes. I am having issue with my workflow though and find myself going in circles as I am not sure how to call the specific gene targets or sequences from my assembly.
Workflow so far: 1. FastQC 2. Trimmomatic 3. FastQC (to verify trimming) 4. Trinity 5. Quality assessment with BUSCO and other methods 6. Salmon (through Trinity) from here I plan on using DESeq2
Also I am using TransDecoder and Trinotate to annotate my assembly (with Blastp, Blastx, and Pfam)
Is there something I may be missing, overlooking, or simply just over-complicating? Is it possible to pull target genes from my assembly and blast them?