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Update canonical transcript overrides with explanation #75

Merged
merged 6 commits into from
Mar 1, 2023
Merged

Update canonical transcript overrides with explanation #75

merged 6 commits into from
Mar 1, 2023

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leexgh
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@leexgh leexgh commented Feb 22, 2023 •
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Fix: genome-nexus/genome-nexus#664

  • Using new oncokb isoform overrides that are extracted from onockb API https://www.oncokb.org/api/v1/utils/allCuratedGenes and separate to grch37 and grch38 files
  • add new columns to explain where does each canonical transcript come from. Options: esembl only one transcript, ensembl longest, uniprot, oncokb, mskcc, manually (stored in genome-nexus-isoform-overrides)

Need to merge #74 first

leexgh
leexgh commented Feb 22, 2023
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data/common_input/isoform_overrides_genome_nexus_grch37.txt
@@ -0,0 +1,3 @@
enst_id gene_name protein_stable_id gene_stable_id comment
ENST00000573679 PTPRC ENSP00000458322 ENSG00000262418
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@leexgh leexgh Feb 22, 2023 •
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This comes from: 88f0d68. @inodb Do you want to add some comments?

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hmm having a hard time reconstructing why i picked that one, maybe ok to leave as is for now

leexgh
leexgh commented Feb 22, 2023
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data/common_input/isoform_overrides_genome_nexus_grch38.txt
@@ -0,0 +1 @@
enst_id gene_name protein_stable_id gene_stable_id comment
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@inodb Do you have more grch38 transcript overrides to add?

inodb
inodb approved these changes Feb 27, 2023
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LGTM - thank you!!

scripts/make_one_canonical_transcript_per_gene.py Outdated Show resolved Hide resolved
@leexgh leexgh merged commit 04e4f1e into genome-nexus:master Mar 1, 2023
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@inodb inodb inodb approved these changes

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Update canonical transcript with new grch37 and grch38 oncokb isoform overrides files
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@leexgh @inodb