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A tool for determining non-canonical splice sites #17

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GallVp opened this issue Apr 17, 2024 · 3 comments
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A tool for determining non-canonical splice sites #17

GallVp opened this issue Apr 17, 2024 · 3 comments
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@jasonshiller @GallVp
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prototyping A tool or a sub-workflow needs prototyping
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0.4.0

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GallVp commented Apr 17, 2024

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@GallVp GallVp added the prototyping A tool or a sub-workflow needs prototyping label Apr 17, 2024
@jasonshiller
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Couldn't find a tool off the rack for this.
Basic workflow I used was:

  • Add introns to the gff3 file from Russell with agat_sp_add_introns.pl
  • Extract the fasta sequences of the introns based on these new features with agat_sp_extract_sequences.pl
  • Python script to extract the first and last 2 dinucleotides of each intron sequence and output genes with non-can splice sites

Workflow is in pangene/prototyping/splice_sites.qmd

@GallVp GallVp added this to the 0.4 milestone Apr 23, 2024
@GallVp GallVp mentioned this issue Apr 23, 2024
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GallVp commented Jun 24, 2024

Added a reusable workflow, PR: https://github.com/PlantandFoodResearch/nxf-modules/pull/25

@GallVp GallVp self-assigned this Jun 24, 2024
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GallVp commented Oct 6, 2024

Completed by https://github.com/PlantandFoodResearch/genepal/releases/tag/0.4.0

@GallVp GallVp closed this as completed Oct 6, 2024
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