Losing Clones

[TheRaspberryFox]

Hello,

I am running TCRdist, and I really like it! Thank you for taking the time to make it.

However, I am noticing that I am losing a considerable amount of my TCRs. As in I have ~2600 clones with complete vdj and cdr3 information, but I only end up with a distance matrix of around 200 clones.

What type of filtering is occurring to make me lose so many clones when running TCRdist. These cells are sorted on tetremer positive cells and also have at least two cells per clone. I also did my own quality control to ensure that they have all information needed. What is causing me to lose so many clones?

Thanks!