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rouskinlab / dreem

Detection of RNA folding Ensembles using Expectation-Maximization (DREEM)
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Unable to use dreem #25

Open dwolf85 opened 1 month ago

dwolf85 commented 1 month ago

Hello,

I am trying to implement the dreem pipeline, but your documentation does not show any use cases, from start to end. I have, with a lot of work, managed to get to the cluster phase (dreem cluster), but I do not understand how to proceed from here, nor what files are supposed to be passed to what tool.

Can you please update your documentation as well as the help of the tools with clear examples, and explain me what to do after the clustering? How do I know how many structures were found, and how do I see their profiles?

Furthermore, I tried to circumvent the issue by using your webserver, but i noticed it is already down.

Thanks.

taillades commented 1 month ago

Hey Matty, could you take a look at this? Thanks :) Best, Yves

Yves Martin +1 857-200-4849 "Sans liberté de blamer, il n'est point d'éloge flatteur"

On Sat, Oct 26, 2024 at 11:02 AM dwolf85 @.***> wrote:

Hello,

I am trying to implement the dreem pipeline, but your documentation does not show any use cases, from start to end. I have, with a lot of work, managed to get to the cluster phase (dreem cluster), but I do not understand how to proceed from here, nor what files are supposed to be passed to what tool.

Can you please update your documentation as well as the help of the tools with clear examples, and explain me what to do after the clustering? How do I know how many structures were found, and how do I see their profiles?

Furthermore, I tried to circumvent the issue by using your webserver, but i noticed it is already down.

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/rouskinlab/dreem/issues/25, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOEXTOWAASVKZZ35ZSR5FRTZ5PKJ3AVCNFSM6AAAAABQVAEUH2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGYYTMMBUGA2TMMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

matthewfallan commented 1 month ago

Hi @dwolf85,

Thanks for your questions. DREEM is obsolete and has been replaced by new software called SEISMIC-RNA (https://github.com/rouskinlab/seismic-rna).

You can find the documentation for SEISMIC-RNA at https://rouskinlab.github.io/seismic-rna/, including a tutorial that involves clustering at https://rouskinlab.github.io/seismic-rna/tutorials/amplicon/index.html.

Sorry for the confusion about this obsolete repository. Please feel free to ask if you have any more questions/concerns about using SEISMIC-RNA!

dwolf85 commented 1 month ago

Thank you both!