Can I use this method to create a cisTarget database for plant?

aertslab / create_cisTarget_databases

Create cisTarget databases

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Can I use this method to create a cisTarget database for plant? #22

Open cheer1104 opened 2 years ago

cheer1104 commented 2 years ago

Hi , I collated the motif information of Arabidopsis thaliana from JASPER database,and I have successfully run the script . I wonder if this method is suitable for the creation of plant cisTarget database? I noticed that 7 species were selected for the rating of motifs. Which 7 species are included?

best, cheer

ghuls commented 1 year ago

The cross-species step is not necessarily required if you have enough motifs. You can run it with cross species with as closely related plant species as possible (under the assumption that closely related species will have the same motifs in conserved regions). If your species are not closely enough related, the results will deteriorate, instead of improve.