To calculate the mean and median fragment length, we reconstruct all of the mRNA transcripts for each clonotype for a given chain and map the deduplicated reads to the reference. If none of the clonotypes map, the fragment length is considered indeterminate. This can result if Archer Analysis cannot reconstruct the transcript. This is rare but if MiXCR (the underlying software used in Archer Analysis Immune Repertoire analysis pipeline) reports a V segment that is not in the MiXCR reference sequence database, the transcript cannot be reconstructed.
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