AssmbleCells Contamination #2108
-
|
Hello, I had two questions regarding clone reports generated from 10X data. and this is a cellranger report of the same sample (filtered_contigs_annotation). The same cell barcode is considered a true cell in Cell Ranger while contamination in MiXCR. What might be contributing to this difference? |
Beta Was this translation helpful? Give feedback.
Replies: 1 comment
-
|
Contamination means that this clone was randomly detected in multiple cells that already have their own chains. Imagine you have 100 cells, each with a unique set of clones, and then one additional clone appears in 80 of those cells on top of their original ones. That clone will be marked as contamination. Contamination is a label applied to a clone, not to a cell. You will likely see other clones associated with the same cell ID that are not labeled as contamination. |
Beta Was this translation helpful? Give feedback.
Contamination means that this clone was randomly detected in multiple cells that already have their own chains. Imagine you have 100 cells, each with a unique set of clones, and then one additional clone appears in 80 of those cells on top of their original ones. That clone will be marked as contamination.
Contamination is a label applied to a clone, not to a cell. You will likely see other clones associated with the same cell ID that are not labeled as contamination.