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vierstralab / motif-clustering

Clustering motif models to remove redundancy
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Is it ok if we don't have <background file> #6

Open Dan-121 opened 2 years ago

Dan-121 commented 2 years ago

Hi, your work is extremely good, and the example is quite good, but I still have some problems. In step 1: Compute pair-wise motif similarity,I wonder if it is necessary for us to give bfile, If so, how can I get this Looking forward to your reply Thank you Dan

Dan-121 commented 2 years ago

plus, I wonder if I can get the V1 code like hierarchical.py.I read a paper that used your tool and provided the code, I wonder if we can offer the V1 code so that I can compare the code to repeat the outcomes in their paper. Thank you.

jvierstra commented 2 years ago

Let me dig up the hierarchical.py script. The background file only has a marginal effect.

duocang commented 2 years ago

@dandata123-tech

i did not dig into it too much. So I do not know if bg file is necessary or not.

But I know how to generate a backgroup file. asta-get-markov or http://rsat.sb-roscoff.fr/create-background-model_form.cgi can do it easily.