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Determine appropriate chimera-checking method for DADA2 and VSEARCH #23

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lina-kim opened this issue Jun 1, 2022 · 2 comments
Open

Determine appropriate chimera-checking method for DADA2 and VSEARCH #23

lina-kim opened this issue Jun 1, 2022 · 2 comments
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analysis-needed Less implementation, more analysis nice to have Stretch goal if time

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@lina-kim
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lina-kim commented Jun 1, 2022

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@lina-kim lina-kim self-assigned this Jun 1, 2022
@lina-kim lina-kim added the nice to have Stretch goal if time label Jun 1, 2022
@lina-kim
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Exposed all relevant chimera-checking parameters for dada2 denoise, and incorporated vsearch uchime-ref. Testing to see which are most helpful for our study.

@lina-kim
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Data waiting to be explored:

  • dada2 denoise run with --p-chimera-method of none, consensus, and pooled
  • All three DADA2 outputs run through vsearch uchime-ref

Also will be helpful to explore error logs and incorporate tests for vsearch uchime-ref wrapper.

@lina-kim lina-kim added the analysis-needed Less implementation, more analysis label Jan 30, 2023
@lina-kim lina-kim removed their assignment Jan 30, 2023
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