Multiple clones per cell barcode

[SirKuikka]

Hi,

I have a simple question. I am looking at the .clones.tsv output for the single-cell Mixcr workflow, and there are often multiple clones per cell barcode. Should I just use the first one with the most reads/UMIs if I want to assign a clone identity to each cell barcode?

[mizraelson]

Hi, what MiXCR version and command do you use?

[SirKuikka]

Hi,

v4.5.0

mixcr analyze %%s -s hsa --rna --threads 4 --force-overwrite %%s_S1_L{{n}}_{{R}}_001.fastq.gz %%s/%%s'%%(preset,gsm,outdir,gsm)

preset was 10x-sc-5gex

The sample I am analyzing is this. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5264643

[mizraelson]

Could you try running the latest version. There should be no more than 2 clones per chain per cell.