Is it possible to upload data to Galaxy directly from Gene Expression Omnibus (GEO)?
I am interested in accessing raw RNASeq data files from published manuscripts that are host in GEO. Is it possible to download them in bulk rather one by one?
Hi @zeylanicus
These reads are in SRA, correct?
That means you can use a tool like this → Faster Download and Extract Reads in FASTQ format from NCBI SRA. Getting Data into Galaxy
These tutorials show some super automated ways to handled batch data. These go from publication identifiers, to read retrieval, through full analysis and graphics. Maybe portions of these you can reuse or customize or just get ideas from. GTN Materials Search (query=sra)
Hope this helps! 