HLA allele from RNA and DNA-seq
2 answers
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?
• 0 views
•
link
updated
by
Ram
•
written
by
Charles Warden
•
written
by
Charles Warden
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.
• 0 views
•
link
updated
by
Ram
•
written
by
Alvaro Sebastian •
•
written
by
Alvaro Sebastian •
Log in to answer this question.
More posts like this
-
PHLAT genotyping with scRNA-seq (10x)
written by malonzm1 •
-
HLA typing with archasHLA - DNA seq?
written by bioinf_sci •
-
small RNA seq on plant
written by m.s_tabatabaei •
-
CNV analysis from exome data
written by vishal •
-
RNA-seq illumina paired-end data simulation with fold change differences
written by k.kathirvel93
-
HLA-VBseq for detecting HLA type using RNA-Seq inputs
written by oghzzang •
-
HLAminer RNA-seq vs Whole exome seq
written by oghzzang •
-
Transcription factor enrichment analysis
written by tarek.mohamed
-
Detection of fusion from a DNA seq file
written by Bioinformatician_in_trouble •
-
phase genotype data (infer haplotypes) for multiple families
written by Teresa •
