ncborcherding
commented
2 years ago Hey Scas224,
Thanks for reaching out. Should have no problems using scRepertoire for data sets with multiple lineages. The error you mention is not related to that and I have not had a reproducible example yet for that to troubleshoot.
I am not sure if multi run provides the individual sample contig annotation files (the newer version might), but scRepertoire does have a function to demultiplex the runs. createHTOContigList() works best if you are using the individual sequencing run before integrating across multiple sequencing runs.
Hope that helps, Nick
Hi! I'm just starting to learn how to use this package in anticipation of data I am going to get from a 10x cellranger multi run, and I am working with some sample data to practice. I was wondering if it is okay to use a seurat object with scRNA data from multiple types of immune cells (macrophages, B cells, platelets, NK cells, and T cells), because obviously not all of these cells are going to match to the VDJ contig data since that is specifically for T cells.
So far it seems to be working and let me use combineExpression, but there are many values in the clonotype columns for the non-T cells, and I am starting to get some errors (such as Error in names(x) <- value : 'names' attribute [3] must be the same length as the vector [0] when trying to use clonalNetwork), and I was wondering if that may be related and could be causing more errors with my analysis.
Is it okay to use a seurat object with all of the cells, or should I subset it to only include the T cells? Thank you for your help!