What is the tool you use for HLA typing from total RNAseq data? I haven’t tried any yet and would be very appreciative for good advice.
Have a look at HLAgenotyper
We performed some search and at this moment we are trying to use OptiType. Based on benchmarks it looks as one of the best for MHC-I. But it doesn’t work with MHC-II.
Will try the HLAgenotyper as well, thank’s.
There is also Seq2HLA which does both MHC I and II. We have had success with it.
Thank’s! Will try it as well.