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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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Old 2.1.5 MixCR version format unsupported #340

Closed KevinMaroney closed 1 year ago

KevinMaroney commented 1 year ago

Hello. I love your tool and would really like to use it with my data. I am unable to use 10X for these samples (very few cells) and therefore have to sort them into individual wells of a plate before sending them to a collaborator in Australia. They have been very helpful in pre-processing (instead of 10X, they isolate TCR's from gels before sequencing them, so I would not really know where to start with their pipeline). However, the version of MixCR they use to pre-process the data in 2.1.5 and thereby the column headers seem to be incompatible with those required by ImmunArch. I am wondering if I can just rename the required columns and it will work? Or if there is a way to make the "older" MixCR format recognizable? Currently I am getting "unsupported format" errors. I have attached an example Excel file (converted to txt in Terminal because I originally thought that was causing problem, though I think ImmunArch accepts whatever file format?).

Sorry for the long rambling explanation. I would really appreciate your help with this :)

KevinMaroney commented 1 year ago

Ci10004-Plate-7-C-E01-CD3-low miXCR clones summary filtered.xlsx.txt

Alexander230 commented 1 year ago

Hello, @SomeGuy3865!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

The file that you've attached is actually in xlsx format, with txt extension. It will not be loaded in Immunarch, please convert it to tsv before loading. Also, please try to install the development version of Immunarch like described here https://immunarch.com/#latest-pre-release-on-github, because it contains some hotfixes for MiXCR format.

I've loaded your attached file successfully with development version of Immunarch after converting it to tsv format.

Best regards, Aleksandr

KevinMaroney commented 1 year ago

Thank you @Alexander230 ! I used the mv command in terminal because I had many .xslx raw MixCR files and wanted to convert all at once. I'll bite the bullet and convert one at a time. I'll also install the development version. Thank you!

KevinMaroney commented 1 year ago

Just updating this. I was able to load in the data. I suppose that my issue was that I thought I could just batch convert my xslx files to txt through terminal but not tsv. Thanks..