HLA typing only based on long-read RNA-seq data?

[yuzhuxuyang]

Hi, according to the paper, it says it support RNA-seq data and long-read sequencing data. I am wondering whether it can do HLA typing only based on long-read RNA-seq data (Oxford Nanopore data)?

[wshuai294]

Hi,

We have not tested SpecHLA on long-read RNA-seq data. But I think it could work. SpecHLA will mask the region with no reads covered, and then perform typing. Please download the latest commit and run python long_read_typing.py -k 5 -g 1, it will afford g-group level results. However, notably, if there is no read covering between exons, it may introduce the switch error.

best,
shuai

[yuzhuxuyang]

Hi Shuai, thanks a lot for the clarification!