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UcarLab / CoRE-ATAC

MIT License
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Can CoRE-ATAC be used for other organisms? #7

Open Galaxy154 opened 2 months ago

Galaxy154 commented 2 months ago

Hello developers,

Very cool tool and great paper.

I was wondering if this tool could be adapted for non-human samples (e.x. cattle)? Or was it specifically developed or trained with hg19 in mind?

Thanks so much!

ajt986 commented 2 months ago

While I did put ways for having CoRE-ATAC function with other genomes, it has not been evaluated for other organisms. Differences in transcription factors and binding site sequences are the main issue here and I predict that mammals would perform better than non-mammals, especially for insulator predictions (CTCF).

I can see two strategies if using CoRE-ATAC:

  1. Training a new model either using the organism of interest in mind, or a model using multiple organisms if training data for the specific organism is absent.
  2. Extracting the ATAC-seq signal-based model that minimally uses DNA sequence for its predictions.