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
Thank you! 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.