MiXCR and Cellranger output differences about mixcr HOT 1 CLOSED

Hi,

To compare results, please use the filtered_contig_annotations.csv output file from CellRanger. In the file you provided (consensus_annotations.csv?), it appears the clones were not separated by cells. Multiple CDR3 entries might be a result of differences in the sequence outside CDR3, but its hard to tell without looking at the actual file.

MiXCR performes various correction and filtering steps to ensure the output TCR/BCR chains are verified. This means that in most cases, if two chains of the same type originate from a single cell ID, there would be a substantial number of reads (UMIs) confirming both. Two chains can indeed be biologically expressed, but contamination can sometimes occur, such as when two cells in a single droplet receive the same cell barcode.

Sincerely,
Mark

from mixcr.