Question: HLA allele from RNA and DNA-seq
0
gravatar for teresa.fazia01
2.3 years ago by
United States
teresa.fazia010 wrote:

Hi everyone,

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

 

Thanks

rna-seq hla dna-seq imputattion • 896 views
ADD COMMENTlink modified 2.3 years ago by Alvaro Sebastian30 • written 2.3 years ago by teresa.fazia010
0
gravatar for Charles Warden
2.3 years ago by
Charles Warden4.9k
Duarte, CA
Charles Warden4.9k wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Charles Warden4.9k
0
gravatar for teresa.fazia01
2.3 years ago by
United States
teresa.fazia010 wrote:

Thanks for your kind reply

 

 

ADD COMMENTlink written 2.3 years ago by teresa.fazia010
0
gravatar for Alvaro Sebastian
2.3 years ago by
Poland
Alvaro Sebastian30 wrote:

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.

 

 

 

ADD COMMENTlink written 2.3 years ago by Alvaro Sebastian30
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