Can xHLA be used for HLA-typing using RNA-Seq data

humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data

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Can xHLA be used for HLA-typing using RNA-Seq data #30

Open raunaq-m opened 6 years ago

raunaq-m commented 6 years ago

Hi I have a large amount of RNA-Seq samples available and was wondering if I can use xHLA for typing? I was not able to find mentions of RNA-Seq data usage in the paper or on the github page.

Could you please indicate if that is possible? Thanks a lot!

tanghaibao commented 6 years ago

@raunaq-m We have not tried it on RNA-Seq, only WGS and WES. It most likely wouldn't work for RNA-Seq since there could be allelic imbalances at the HLA loci.

icymiktreize commented 6 years ago

Hi, how about amplicon sequencing data for a specific HLA locus?