We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and ...
HLA typing from RNA-Seq sequence readsGenome Med, 2012,4(12):102. URLPMID:23259685 We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped...
Article (Boegel et al., 2013) HLA typing from RNA-Seq sequence reads. Genome medicine. PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/23259685 URLhttps://bitbucket.org/sebastian_boegel/seq2hla 源代码,下载并安装 https://bitbucket.org/sebastian_boegel/seq2hla/src http://tron-mainz.de/tron-fa...
HLA typing from RNA-Seq sequence reads. Genome Med. 2012;4(12):102. 23. 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. 2014;15:325. 24. Kim HJ, Pourmand N. HLA haplotyping from RNA-...
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A catalog of HLA type, HLA expression, and neo- epitope candidates in human cancer cell lines Sebastian Boegel ab , Martin Löwer a , Thomas Bukur ab , Ugur Sahin abc & John C Castle a a TRON gGmbH - Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH; ...
et al. HLA typing from RNA-Seq sequence reads. Genome Med 4, 102 (2013). https://doi.org/10.1186/gm403 SOAP-HLA Cao H, Wu J, Wang Y, Jiang H, Zhang T, et al. (2013) An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region ...
HLA typing using RNA-Seq data The tool seq2HLA v2.2 (https://github.com/TRON-Bioinformatics/seq2HLA) was used to derive HLA class I (classical and non-classical) and class II types from the RNA-Seq data. Seq2HLA v2.2 previously determined 4-digit resolution HLA types with high accuracy...
The options for partial typing are the same as genotype. Partial typing can be run from the intermediate alignment file. Merge jsons To make analysis easier, this command will merge all jsons produced by genotyping into a single table. All.genotype.jsonfiles will be merged into a singlerun....
Boegel S, Lower M, Schafer M, Bukur T, de Graaf J, Boisguerin V, Tureci O, Diken M, Castle JC, Sahin U: HLA typing from RNA-Seq sequence reads. Genome Med. 2013, 4 (12): 102- Article Google Scholar Kim HJ, Pourmand N: HLA haplotyping from RNA-seq data using hierarchical re...