COMBINE-lab/salmon

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

Opened this issue · 0 comments

Cellecta commented

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
image

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
Add any other context about the problem here.