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Add support for alevin backend #62

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5 tasks
mfansler opened this issue Aug 4, 2023 · 2 comments
Open
5 tasks

Add support for alevin backend #62

mfansler opened this issue Aug 4, 2023 · 2 comments
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enhancement New feature or request

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@mfansler
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mfansler commented Aug 4, 2023

Users may prefer to use Alevin as the quantification backend as it offers an alternative deduplication model. Multiple tasks are necessary to establish this:

  • add a new configuration key, e.g., backend that accepts either: "kallisto-bustools" or "alevin"
  • create UTRome indices (mouse, human) for alevin, possibly with genomic decoy
  • implement downloading rules (probably should do this as part of snakemake all the things #51)
  • implement quantification rules
  • implement output rules
@mfansler mfansler added the enhancement New feature or request label Aug 4, 2023
@a2672
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a2672 commented Dec 18, 2024

Do you have the human UTRome index created for alevin?

@mfansler
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No, this has not been created yet.

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