how to export full BCR receptors with mutated nt? #1069
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Is this true? Thanks! |
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Hi, Regarding your question:
https://mixcr.com/mixcr/reference/mixcr-export/#export-contigs-with-imputation When you use If you are looking for a full-length BCR receptor reconstruction you want to specify I can help you with the command for a new MiXCR. Can you tell more about the cDNA library architecture that you use? Is it a commercial kit or a custom protocol? |
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Hi,
First of all, judging by the command, I think you use an outdated version of MiXCR. I would strongly recommend updating to the latest version as it has lots of improvements.
Regarding your question:
mixcr exportClones -p fullImputed
returns clonotype tables with gene features imputed with germline nucleotides if a particular region (or a part of the region) is not covered. Lets say you library only partially covers FR1 region of V gene, then-p fullImputed
will return the FR1 with capital letters for the part covered with the read and lower case letters imputed from the germline. In other words imputation doesn't have anything to do with hypermutations.https://mixcr.com/mixcr/referen…