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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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MiXCR import no longer works #401

Closed MikolajKocikowski closed 5 months ago

MikolajKocikowski commented 5 months ago

🐛 Bug

Hi, I keep getting an error trying to load any MiXCR output to Immunarch. The message "Samples found in the metadata, but not in the folder" is not helpful, but the issue I think is that Immunarch requires the clones.txt files from MiXCR, but MiXCR outputs clones.tsv files now, which differ in content and are not recognized. Is exporting-importing airr fles the recommended solution now, or is there another way to make these compatible? Thanks

vadimnazarov commented 5 months ago

Hi, could you try to export MiXCR files in the AIRR format please? We are working on the next version of Immunarch, and consider dropping the support for non-AIRR standard formats as they are too cumbersome to support.

vadimnazarov commented 5 months ago

(responded to you on Linkedin)

MikolajKocikowski commented 5 months ago

Hi, thanks for the reply and that's great news - looking forward to the next release!

I apologize I forgot to close this issue - I finally figured out I can import new MiXCR files just as well as airr - but both only when the files have some specific names and not others... Opened another issue about this, co closing here.

vadimnazarov commented 5 months ago

No worries! We have reserved only the "barcode" and "metadata" filenames. I hope we will be more verbose about this in the next version.