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Salmon alevin cannot work well with 10X 3' V4 data #949

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Cellecta opened this issue Aug 2, 2024 · 0 comments
Open

Salmon alevin cannot work well with 10X 3' V4 data #949

Cellecta opened this issue Aug 2, 2024 · 0 comments

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@Cellecta
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Cellecta commented Aug 2, 2024

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
alevin
Describe the bug
I got reasonable cell barcode when I worked with 10X cellranger, I just got very few cell barcode when I use alevin. I don't have problem with 10X V3 data when I use alevin.

To Reproduce
Steps and data to reproduce the behavior:

Specifically, please provide at least the following information:

  • Which version of salmon was used?
  • How was salmon installed (compiled, downloaded executable, through bioconda)?
  • Which reference (e.g. transcriptome) was used?
  • Which read files were used?
  • Which which program options were used?

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
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Desktop (please complete the following information):

  • OS: [e.g. Ubuntu Linux, OSX]
  • Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]

Additional context
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