If I want to get multiple RNA-seq FASTQ files from repositories (ENA or GEO, etc), what is the best way to go about this?
So far, what I do is, I find a paper, look at the GEO #, go to GEO page and get BioProject #, go to ENA, and then download the files. And essentially, if I wanted to do this for 5 papers, I would have to repeat the steps x5.
I have a list of genes that I'm interested in, and want to know how they have changed in RNA-seq profiles to determine how they change (before I decide whether or not doing my RNA-seq may be worthwhile). I know there are repositories that clump large # of data sets together but I want to know how to do it myself since I may only want to look at selected sets of RNA-seq (ie top 10 data sets most relevant to my experiments).