Question: RepeatExplorer2 clustering: The number of sequences analyzed is very low
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gravatar for agostinifede
6 months ago by
agostinifede0 wrote:

Hello! In RepeatExplorer2 clustering, I need to work with 90,000,000 sequences. Is there the possibility of configuring some parameter to work with the total number of sequences? In Sample Size, I put the 90,000,000 sequences, but the number of sequences analyzed is significantly reduced. Can something be done to increase the number of sequences analyzed? Thank you!

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by agostinifede0
2
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This tool is not wrapped and in the Main Tool Shed (MTS), so we cannot comment directly on how to modify the tool wrapper/set parameters. This may be an upper limit in the underlying tool or how the server's administrators configured the tool when hosted publically.

I would suggest contacting the administrators of the server you are working on to find out if this is an end-user configurable option or not.

If you working here https://galaxy-elixir.cerit-sc.cz/, server information and help FAQs are here http://repeatexplorer.org, with another summary available in the Galaxy hub here: https://galaxyproject.org/public-galaxy-servers/repeatexplorer/. There isn't a direct user support contact made public, except for what is available here: http://w3lamc.umbr.cas.cz/lamc/?page_id=301. So, try using the corresponding author contact associated with the related publications, or contact this lab's scientists/admins directly, to get specifics for usage recommendations plus information about any server-side administrator settings at the public Galaxy site they host.

The above advice is applicable for all custom tools, that are not in the MTS, yet available at public Galaxy servers. Each is hosted/configured independently.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k

Hello Jen,

Thank you for your answear. I contacted the author and got the help I needed. Thank you for being so active and helpful in this forum.

Federico.

ADD REPLYlink written 6 months ago by agostinifede0
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