You want to have reads in FASTA format? I don't think they store it that way. But you can convert fastq to fasta.
I tired to convert from Fastq to Fasta. however, the result is not matching with Mirdeep ( I'm trying to follow galaxy tutorial for miRNA analysis). SRA does provide an option to directly download in Fasta, but I can't find an option here, unfortunately.
@bgruening:matrix.org Hi Björn, I get an "Internal Server Error" when trying to export a history into a workflow. Any insides? I would like to export all tools and settings to the workflow to publish it alongside a Revised Manuscript.