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I am using mixcr to convert fq.gz raw data file (single cell BCR sequencing) to txt files with the names such as JX01_d3-B.clonotypes.IGH.txt , Then I use the immunarch to load the file to explore the clonotype and clonarity of the reportiore. However, I found many BCR clone numbers are very large that can exceed 2 million. As far as I understand, each individual B cell can only have one clonotype, the total number of single cells for one sample is no more than 10 thousands (10000). How can the database generate so large number of BCR clones?

screen shot for the results enter image description here

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  • $\begingroup$ Just a guess, but, are you sure of what those columns signify? It looks like you have at most 645 rows for sample HZ01_d5-B, even though those numbers in the second column go up to over 2 million (that is, they're not at all contiguous). Could those be clone ID numbers, and the third column the counts per ID? And then for JX01_d1-B, it starts with the most abundant clone as #1 with a count of 183, and the counts decrease again? I'd compare what you're seeing with mixcr's documentation. $\endgroup$
    – Jesse
    Aug 30 at 19:53

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