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TO-DO before upcoming release #969

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5 tasks
katsikora opened this issue Jan 23, 2024 · 0 comments
Open
5 tasks

TO-DO before upcoming release #969

katsikora opened this issue Jan 23, 2024 · 0 comments

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@katsikora
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katsikora commented Jan 23, 2024 •
edited

  • createIndices: drop 'gtf to files', use gtfToGenePred instead? (would be consistent with repoTrampoline)
  • take transcript2gene.txt as input to Salmon_Alevin ("genes_t2g")
  • drop gene symbol annotation from velo_to_sce ? (scRNAseq_splitAlevinVelocityMatrices.R) - would relieve the requirement from gene ID to gene symbol mapping
  • keep filterGTF and all downstream functions only for counting, not for mapping steps (or disable completely?)
  • create salmon indices and update organism yamls
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