I am trying to use plotDEXseq, but the rds file generated from my DEXseq job does not automatically populate the input field. If I select it from a browsing menus, “(unavailable)” appears before the file name.
Galaxy doesn’t assign a database attribute during Upload unless that is specified by the user. The default is no assignment.
Galaxy might assign a database attribute for other types of jobs, example = mapping job. The assigned database would be with respect to the genome/build for the reference genome mapped against.
Some tool use or require that database attribute to access built-in indexes. If that database assignment isn’t an indexed database, or the assignment is a mismatch for the data content of the file (chromosome names/coordinates differ), expect mismatch errors or odd results.
For the human GRCh38/hg38 genome assembly/build, the version indexed on the public servers is: hg38 and was originally sourced from UCSC.
This can get more complicated (custom genome, custom build, custom database/dbkey). This forum has much help for those topics if needed but might not be needed. Let us know if you need more help.