Thank you both for your answer !
I do have an affiliation with a research institute linked with an hospital, but the access to a bioinformatic server from outside the institute still have to be discussed. You confirm my fear that most public accessible data are raw data.
I used galaxy before with Chip-seq data, but I had access to an institutional galaxy plateform. Now I would only have access to the open access, meaning that have a 250 GB of data limitation.
Another limitation might be network connectivity : Network is pretty bad here, may be upgraded, but for now, exchanging GBs of data is out of question...
What you said WouterDeCoster about original Pipeline is interesting. I don't see any reason why I should follow the paper pipeline if there is new/better available approach.
What about Bioconductor ? Is RNAseq analysis with R possible ? Does it make sense in term of computing power ?