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deepomicslab / SpecHLA

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
MIT License
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HLA typing only based on long-read RNA-seq data? #25

Closed yuzhuxuyang closed 5 months ago

yuzhuxuyang commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

Hi Shuai, thanks a lot for the clarification!