Question: Problem with the tool: Extract Genomic DNA
2
gravatar for mariane.cfugulin
6 weeks ago by
mariane.cfugulin20 wrote:

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!!

Mariane

extract galaxy chip-seq • 129 views
ADD COMMENTlink modified 12 days ago by Jennifer Hillman Jackson25k • written 6 weeks ago by mariane.cfugulin20
1

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.

ADD REPLYlink written 12 days ago by fzguo10

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

ADD REPLYlink written 12 days ago by Jennifer Hillman Jackson25k

Hi Jen, mm10 does not work either. Would you please fix this tool in the near future? Thanks FG

ADD REPLYlink written 9 days ago by fzguo10
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