Heavy or light chain of BCR CDR3

[seongguheo]

Dear Authors,

Hello,
I am looking at Smart-seq2 full length scRNA-seq data for BCR CDR3 clonal sequence.
I wonder which one, heavy or light chain, does mixcr use to predict CDR3 sequence.
Is there any preference to chose the chain?
Please, have a look the below, some of the clones.tsv file of my analysis.

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aaSeqCDR3  allVHitsWithScore allDHitsWithScore               allJHitsWithScore allCHitsWithScore
1    CQQSYSLPLTF IGKV1-3900(392.2)                                   IGKJ400(188.1)    IGKC00(230.3)
2   CQSYDTSLSGVF IGLV1-4000(461.1)                                   IGLJ300(213.4)   IGLC300(215.9)
3   CASYTITLTYVF IGLV2-1400(385.8)                                   IGLJ100(184.8)   IGLC100(198.7)
4    CQQYNTYPWTF  IGKV1-500(290.7)                                   IGKJ100(189.5)      IGKC00(181)
5 CQVWETSGDPYVVF IGLV3-2100(566.1)                                   IGLJ200(176.1)   IGLC200(173.8)
6   CSSYTNSRSWIF IGLV2-1400(682.4)                   IGLJ300(165.5),IGLJ200(164.6)   IGLC2*00(176.4)

Many thanks,
Luke

[mizraelson]

Hi,
The choice between heavy and light chain depends on the covered V and J genes. mixcr uses all chains references (for the selected species) to align the reads and then assembles the clones accordingly.