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make gene_name field in transcript annotation GTF optional #20

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dlaehnemann opened this issue Aug 22, 2022 · 0 comments
Open

make gene_name field in transcript annotation GTF optional #20

dlaehnemann opened this issue Aug 22, 2022 · 0 comments

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@dlaehnemann
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Currently, we have to work around this by excluding any GTF entry that does not have the gene_name set:

https://github.com/snakemake-workflows/dna-seq-neoantigen-prediction/pull/23/files#diff-bdbc470ee4d301e2056eeaa242d0abb73fd5995234758137dd4b6b2e31a602dcR47-R56

However, gene_name is "only" the common gene name, and in all the cases I found, a Ensembl gene_id was always present, even if no gene_name was there. Thus, as long as we ensure that gene_id is set, making gene_name optional should be no problem.

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