Question: Problem with the tool: Extract Genomic DNA
2
gravatar for mariane.cfugulin
5 months 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 • 355 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 5 months 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 3 months 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 3 months 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 3 months ago by fzguo10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour