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 ...
Table 1 Comparison of HLA typing software 软件原理分辨率数据类型是否测试参考文献 NGSengine 8-digit Amplicon Y - HLAminer 比对/组装 4-digit WGS/WES/RNA-seq/amplicon Y [18] ATHLATES 组装 4-digit WGS/WES/amplicon N [19] HLAFOREST 比对 4-digit RNA-seq N [20] OptiType 比对 4-digit WGS...
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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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...
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; ...
seq2HLA Boegel, S., Löwer, M., Schäfer, M. 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 ...
Paired-end RNA-Seq sequence reads for 4340 samples, representing 38 tissues and 17 cell types (Additional file1: Table S1),sequenced with the Illumina platform were downloaded from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) and European Genome-phenome Archive (EG...
In order to test arcasHLA partial typing, we need to roll back the reference to an earlier version. First, fetch IMGT/HLA database version 3.24.0: ./arcasHLA reference --version 3.24.0 Extract reads: ./arcasHLA extract test/test.bam -o test/output -t 8 -v ...