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Incorporate Genome ID (tag) into gene IDs and other gene features #135

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jasonshiller opened this issue Feb 4, 2025 · 2 comments
Open

Incorporate Genome ID (tag) into gene IDs and other gene features #135

jasonshiller opened this issue Feb 4, 2025 · 2 comments
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enhancement New feature or request

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@jasonshiller
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Description of feature

Currently genes in genepal outputs do not encode the genomeID associated with the annotations.

e.g gene1 (gene)
gene1.t1 (mRNA)
gene1.t1.cds1 (CDS),
gene1.t1.exon1(exon)

To enable easier downstream processing and less confusion I suggest adding a genomeID (tag from the assembly sheet) prefix to these entries.

e.g. CK51_09_hap1.gene1
CK51_09_hap1.gene1.t1
CK51_09_hap1.gene1.t1.cds1
CK51_09_hap1.gene1.t1.exon1
@jasonshiller jasonshiller added the enhancement New feature or request label Feb 4, 2025
@GallVp
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GallVp commented Feb 4, 2025

Should we add a pipeline parameter which enables/disables this feature? --include_assembly_tag_as_id_prefix

@jasonshiller
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Yes, I think that might be useful for some people

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@jasonshiller @GallVp