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data-fun / 3d-genome-builder

3DGB is a workflow to build 3D models of genomes from HiC data
BSD 3-Clause "New" or "Revised" License
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How can I use outputs of HiCPro to predict 3D models? #8

Open GleeenSIBS opened 1 year ago

GleeenSIBS commented 1 year ago

Hello~ This is a wonderful tool for people who are in the field~!

I already have the final outputs of HiCPro (such as .matrix and _abs.bed ), I don't need to run HiCPro again through 3d-genome-builder. So, how can I use 3d-genome-builder to predict the 3D structure of chromatins?

pierrepo commented 1 year ago

Hello @GleeenSIBS Thanks for your interest in 3DGB.

The workflow is currently fully integrated, meaning it is not possible to plug in already generated files such as matrix files. We designed the workflow this way to ensure solid consistency along the entire procedure, avoiding extra quality check at intermediate steps. For now, the only possibility is to run the workflow from scratch, starting with FASTQ and genome files.

However, your query is absolutely valid and we will keep it in our backlog.