Hello all,
I am currently trying to find the most efficient way to obtain RNA-seq data for input into a co-expression network. This means I'll be downloading multiple runs from ~50 experiments (~700 runs in all). So far it has seemed like SRAdb is the best way to do this, by bulk-selecting and downloading experiments that use the instrumentation/species/etc that I need. However, I can't seem to find the metadata location for sample/run phenotype! Most fields in the "sample_attribute" column are NA, same with "run_attribute".
I was really hoping to be able to automate the process of assigning control vs treatment groups for purposes of differential expression analysis. Is this even possible from within SRAdb, or will I just have to follow url links to the study information?
Thanks,
Maureen
