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
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.
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:
Expected behavior A clear and concise description of what you expected to happen.
Screenshots
Desktop (please complete the following information):
sw_vers. If you are on linux the output ofuname -aandlsb_release -a]Additional context Add any other context about the problem here.