I am trying to reconstruct full heavy and light VDJ sequences from lymphoma samples (bulk). Normally it should not be very clonal, so most of the reads should derive from the same sequence. TruSeq RNA sample preparation v2, 75bp single end reads.
I tried different pipelines with MiXCR, but I never get more than half of FWR3 and complete CDR3.
Has anyone ever tried this? I am unsure whether it’s even possible to get a longer assembly, but I also don’t see a reason why the information should not be contained in my reads.
Or is it maybe worth trying one of the single-cell reconstruction tools?