I am using Galaxy to analyze some RNA-seq time-course experiments. These exp's involve monitoring the induction of a viral transgene (and other genes that are coordinately induced) when compared to uninduced controls in a transgenic organism.
How do I go about adding my transgene and promoter to the genome.fa and genes.gtf files so that its induction is visible in the results?
Do i even need to do this to see this data?
Can you recommend some references that address the issue of using Galaxy in the analysis of RNA-seq data from transgenics?