Just read on the Salmon genome sequencing efforts, you are correct there is no annotated genome yet, and this will be annoying.
You may need to use a de novo transcriptome (created with Trinity Oases, transAbyss), after aligning your RNASeq reads. I also believe Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html) can work without an annotation (confirmation, anyone?). Anyway, this step should yield a transcripts.fa file with the genomic sequences of the transcripts you want to quantify.
Use Devon Ryan's advice for finding differentially expressed transcripts. You will then need to identify your differentially expressed transcripts in order to match them to a metabolic process.
This article http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368115/ is about the Rainbow Trout which is also a member of the Salmonidiae. It might be of interest to you in terms of material/methods, and as a relatively close species.
modified 3.9 years ago
3.9 years ago by
cyril-cros • 890