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pachterlab / seqspec

machine-readable file format for genomic library sequence and structure
MIT License
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DNA for modalities #26

Closed visze closed 11 months ago

visze commented 11 months ago

I try to create a seqspec file for MPRAs. for teh aqssignment sequencing we are sequencing genomic/synthetic regions which we designed and the BC which is associated with. So I would say this is sequencing of a DNA modality. But seqspec allows only this:

'DNA' is not one of ['rna', 'tag', 'protein', 'atac', 'crispr'] in spec['modalities'][0]

None of them fits to the modality in our case

visze commented 11 months ago

Same for region_type. Because not every designed sequence is a "real" genomic sequence gDNA I would rather use DNA than gDNA. but DNA is not allowed

sbooeshaghi commented 11 months ago

Good idea to have dna as one of the modalities and region_types. Can you put in a pull request to the spec and I can review and accept?

sbooeshaghi commented 11 months ago

I've gone ahead and added dna to both region_type and modalities in the most recent commit.

https://github.com/IGVF/seqspec/commit/5f17ffcfb11aef35d43166f16488164f15f13451