10X sc TCR sequencing outputs about mixcr HOT 2 CLOSED

Bumping this! I would also really like to know how any multi-chain clonotypes are identified!

from mixcr.

Hi,

• By default, MiXCR utilizes its own built-in library. However, if required, you can use IMGT.

• MiXCR automatically calculates dynamic thresholds for Reads per UMI, UMIs per cell, and several other advanced filters. These filters are determined based on the barcode distribution in each sample to optimize performance when applied collectively. Filtering all cells by a fixed number of reads (e.g., 25) wouldn't be suitable in many scenarios. While it's possible to write a new preset to hardcode a 25 reads/cell limit, I'd strongly advise against it. Based on our experience, the filters we employ provide more accurate immune repertoire analysis.

• The grouping algorithm operates in the following manner: We first filter out non-productive clones and cell barcodes that combine chains, which are obviously from duplets (e.g., a combination of TCR and BCR or IGK and IGL in a single cell). Clones are then grouped by CELL barcodes. Subsequently, we attempt to merge cell groups, adding to the most substantial group any group that is fully encompassed by the target. This method results in the formation of cell groups sharing the same chains. We plan on refining this algorithm in the next release to better cater to data with significant noise.

Sincerely,
Mark

from mixcr.