I am new to BCR seq. and we are going to use multiplex PCR protocol to detect incomplete IgH(D-J) and by Illumina Hiseq 150*2 in B-ALL patients. Since we are amplifying BCR (DNA) without V segment, can I still use MiXCR to process the data? If yes, which parameters I must use in the alignment?
Previously I just have used 5RACE method and RNA as input for the BCR seq.
Thank you very much!