Hi! I'm new with bio-info analysis and I'm doing my first ChIP-Seq analysis with Galaxy. I followed the https://galaxyproject.org/tutorials/chip/ to have a step-by-step protocol that I adjust with my samples.
Since the start, I'm using the database: mm10 with no problem, but now that I'm using the "Extract Genomic DNA using coordinates from assembled/unassembled genomes (Galaxy Version 3.0.3)". I need to choose a source for the reference genome, locally cached (like in the example of the tutorial) but I need to enter a "Parameter reference_genome requires a value, but has no legal values defined." ... what am I supposed to enter? Because mm10 doesn't work and I try a lot of combinaison!! What value am I supposed to enter?
Thank you so much in advance for help!!
Have you figured out the solution? I have the same problem - "Parameter reference_genome requires a value, but has no legal values defined.". I tried different combinations and it did not work.
There does seem to be a tool problem.
This happens even when the input is assigned to a database and that database is indexed on the server (or at least at Galaxy Main https://usegalaxy.org). The genome mm10 should be fine. For genomes not indexed on the server, a custom genome can be used.
More feedback soon. Jen, Galaxy team
Hi Jen, mm10 does not work either. Would you please fix this tool in the near future? Thanks FG