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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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how to add both vdj_B and vdj_T same time #34

Closed Lei-GitHub closed 1 year ago

Lei-GitHub commented 1 year ago

Hi, I want to try the method VDJ_GEX_matrix, I have vdj_b and vdj_t, GEX and feature antibodies. Can I call VDJ_GEX_matrix same time, How to do that? I see the parameter VDJ.out.directory.list, Is that I only can add one VDJ data to VDJ_GEX_matrix function? Thank you very much. Best, Lei

vickreiner commented 1 year ago

Hi Lei,

the VGM function can handle input from both B and T reperoires in the same run and compile a common matrix. We do not recommend this though, because following analysis functions (e.g. clonotyping, abundances) are not build to run B and T repertoires in the same call.

You can run the VGM twice, providing the same GEX and Feature Barcode input directories and changing only the VDJ input directories to include only T or B cells. The VDJ.out.directory.list lets you add as many Cellranger VDJ output directories as you wish. Hope this helps, please let us know if you encounter any issues!