Question

HLA allele from RNA and DNA-seq

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9.3 years ago

Teresa ▴ 20

Hi everyone,

Can you please suggest me some software for HLA imputation from DNA and RNA-seq.

Thanks

hla imputation DNA-seq RNA-Seq • 2.7k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Teresa ▴ 20

Ram · Answer 1 · 2015-08-04

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9.3 years ago

Charles Warden 8.3k

You might want to check out this post (I think most tools are designed with DNA-Seq in mind, but they might also work with RNA-Seq): Software For Hla Typing Using Ngs?

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Charles Warden 8.3k

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Thanks for your kind reply

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Teresa ▴ 20

Ram · Answer 2 · 2015-08-06

Check this article: Bai, Y., Ni, M., Cooper, B., Wei, Y. & Fury, W. Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. BMC Genomics 15, 325 (2014).

They describe their algorithm PHLAT (in my opinion, overrated), but they mention other available tools: HLAminer, HLAforest, seq2HLA. Check the latest versions of these tools.

Good luck.