Optitype hla分型结果

Author: yuzc

August undefined, 2024

Web最近又被抓去做HLA分型，由于各种原因之前通过singularity安装在超算上的optitype用不了了，只好用conda安装optitype再解决之前说的conda安装后的报错问题了。我首先是在超算上进行了optitype的conda安装，装好之… WebJan 8, 2015 · HLA（human leukocyte antigen ，人类白细胞抗原）是人类的主要组织相容性复合体（MHC）的表达产物。. 通常也称为人类主要组织相容性复合物 (MHC)，在染色体 …

基于DNA或RNA的NGS数据进行HLA分型 - Zhongxu blog

WebJun 25, 2024 · Results: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific … WebMar 7, 2024 · OptiType(2014年) —— 基于整数线性规划的HLA基因分型算法 [PMID: 25143287] xHLA (2024年) [PMID：28674023] （听说对硬件要求较高; HLA-HD (2024年) … how many middle schools in jcps

人类白细胞抗原（HLA）基因分型 - 简书

WebDec 1, 2014 · We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not … WebBackground The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if … Web1991年第11届国际hla专题讨论上提出了hla的dna分型方法，这类方法近年来在研究和应用方面发展非常快，有取代其他方法的趋势。dna分型方法主要分为两种：基于核酸序列识别 … how many midges in scotland

OptiType: precision HLA typing from next-generation sequencing …

Investigations of sequencing data and sample type on …

WebAug 20, 2014 · Result: We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not … WebAug 20, 2014 · To summarize, OptiType is a fast and accurate HLA typing method based on NGS data, which provides an alternative approach to common HLA genotyping methods. It can be easily adapted to predict genotypes for loci other than HLA-I such as HLA-II and transporter associated with antigen processing. how are parks sustainableWebMay 20, 2024 · The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions … how many midfield players passed out

"WebJun 10, 2024 · OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. Environment Modules. Run module spider optitype to find out what environment modules are available … " - Optitype hla分型结果

Optitype hla分型结果

OptiType: precision HLA typing from next-generation

WebMay 10, 2024 · HLAminer软件可以同时对HlA I型基因和II 型基因进行分型，但是分型结果中不可避免的会存在假阳性的结果。. 为了提高分型结果的准确性，不同的研究团队都在开 … WebJan 8, 2015 · HLA-I类基因分型软件-Optitype介绍. HLA（human leukocyte antigen ，人类白细胞抗原）是人类的主要组织相容性复合体（MHC）的表达产物。. 通常也称为人类主要组织相容性复合物 (MHC)，在染色体 6p21.3 上包含一个 4 Mb 的区域，其中包含 200 多个基因。. HLA根据不同的基因位 ...

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OptiType uses the following software and libraries: 1. Python 2.7 2. RazerS 3.4 3. SAMtools 1.2 4. HDF5 1.8.15 5. CPLEX 12.5or other Pyomo … See more Optional step zero: you might want to filter your sequencing data forHLA reads. Should you have to re-run OptiType multiple times on the same sample(different … See more OptiType is a novel HLA genotyping algorithm based on integer linearprogramming, capable of producing accurate 4-digit HLA genotyping predictionsfrom NGS data by simultaneously … See more WebOct 1, 2024 · For the individual loci, HLA-A, -B and -C, Optitype’s typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools’ robustness to lower DOC data ...

WebDec 1, 2014 · To summarize, OptiType is a fast and accurate HLA typing method based on NGS data, which provides an alternative approach to common HLA genotyping methods. … WebApr 25, 2024 · HLA分型. LOHHLA需要的输入文件中除bam外，还需要HLA Class I的分型结果以及肿瘤倍性与纯度信息。其中HLA分型可使用Optitype、Polysolver、HLA-HD …

WebOct 1, 2024 · The availability of HLA genotyping was the highest in the OptiType tool for all HLA-A, C, and B types, and the values were 99.1% for HLA-A, 99.4% for HLA-B, and 100% for HLA-C. In HLA-A and HLA-C, Kourami showed the lowest availability, and the values were 72.6% and 72.5% in each. WebOptiType. OptiType is an HLA genotyping algorithm based on linear integer programming. It provides accurate 4-digit HLA genotyping predictions from NGS data. For further reading and documentation see the OptiType documentation. The pipeline results contain a CSV file with the predicted HLA genotype. Each line contains one solution with the ...

WebAug 20, 2014 · OptiType (v1.3.3) [37] was performed on germline pairedend whole-genome sequencing fastq files after fishing for HLA reads at 95% identity, taking only the top match with razers3 (v3.5.8) [38 ...

WebOct 11, 2024 · OptiTypePipeline.py -i read_1.fq read_2.fq --dna -v -o optutype. 1. AMD YES的r7-4700u加持下，在近乎突破硬件极限的情况下完成了分型。. 结果首先是个pdf文件，是 … how are partials fittedWebDec 17, 2024 · 상기 방법은: 피검체 유래의 생물학적 시료로부터 획득된 DNA 또는 RNA에 대한 염기 서열 분석을 수행한 결과를 획득하는 단계, 및 OptiType, HLA-HD, PHLAT, HLAscan, 및 HLA*LA 중 3개 이상의 툴(tool)들을 사용하여, 상기 염기 서열 분석의 결과로부터 HLA 타입을 결정하는 ... how are participants selected for a study how are particles in slime arrangedWeboptitype¶ Precision 4-digit HLA-I-typing from NGS data based on integer linear programming. Use razers3 beforehand to generate input fastq files only mapping to HLA-regions. how many middle schools in frisco isdWeb2.optitype输入文件【存储空间占用低】：可以先在超算上对WES/RNA-Seq测序数据进行razers3比对提取和samtools格式转换(详见之前的文章生科院的老张：服务器singularity … how many midgets work in the nflWeb我们首先使用 HLA-HD、Athlates 和 OptiType 对 HLA 的 I 型和 II 型共计 12 个标准品分析，具体结果见表 3。 HLA-HD 和 Athlates 比 OptiType 的 HLA I 型分型更加准确，两者仅 … how many midfielders in soccerWebMar 1, 2024 · HLA genotypes were predicted from the RNA-seq fastq file using the Optitype, and MHC-I binding predictions for the filtered peptides were predicted with netMHCpan4.1. As a result, an average of 3518 and 932 candidate neoantigens were obtained in the two cohorts, respectively ( Tables S4 and S5 in the Supplementary Materials ). how many midichlorians does vader have