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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Getting intuition #32

Closed MaryGoAround closed 1 year ago

MaryGoAround commented 1 year ago

Hello team

I read in your vignette that 10x genomics cellranger returns some output from count for GEX (5' and 3') and VDJ for enriched immune receptor libraries which could be visualized by Platypus, etc

So, having this, what is the purpose of tools like mixcr please? I mean, when 10x genomics cellranger gives these things why you use mixcr in a part of vignette?

Am I right mixcr and cellranger can do the same tasks?

Sorry I am very naive in immunology

Thanks for any help in advance

vickreiner commented 1 year ago

Hi,

I dont know if I have fully undestood the question. MiXCR is primarily an alignment tool and in Platypus we really only use it extract VDJ segment annotations (FR1, CDR1 etc.) and get a trimmed reference for each receptor. The capabilities of Mixcr go well beyond that and do overlap with other tools such as Cellranger as wells as Trust4 Hope this helps!