I’m trying to run GOSeq with human RNA Seq data that has been processed with Salmon, summarized to gene level with tximport, and DGE run using DeSeq2.
I was reading the vignette for GOSeq and got stuck/confused on the part where you need to know what human genome build you used... It says you need to know this to access the correct transcript length in their database.
This may be a stupid question/lack of understanding on my part...But with Salmon/tximport I do not have this information because I did not map to a specific genome, correct? So then could I just use the avgTX length from the tximport function to input to GOSeq to correct for length biases?